diff --git a/NAMESPACE b/NAMESPACE
index 76467677..186ca517 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,8 +5,10 @@ export(IPG2Lineage)
 export(acc2FA)
 export(acc2Lineage)
 export(addLeaves2Alignment)
+export(addLeaves2Alignment_legacy)
 export(addLineage)
 export(addName)
+export(addName_lecacy)
 export(addTaxID)
 export(alignFasta)
 export(assignJobQueue)
@@ -24,6 +26,7 @@ export(combineIPR)
 export(condenseRepeatedDomains)
 export(convert2TitleCase)
 export(convertAlignment2FA)
+export(convertAlignment2FA_legacy)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
 export(countByColumn)
@@ -48,6 +51,7 @@ export(filterByFrequency)
 export(findParalogs)
 export(formatJobArgumentsHTML)
 export(generateAllAlignments2FA)
+export(generateAllAlignments2FA_legacy)
 export(getAccNumFromFA)
 export(getProcessRuntimeWeights)
 export(getTopAccByLinDomArch)
@@ -99,7 +103,9 @@ export(writeMSA_AA2FA)
 export(writeProcessRuntime2TSV)
 export(writeProcessRuntime2YML)
 importFrom(Biostrings,AAStringSet)
+importFrom(Biostrings,readAAMultipleAlignment)
 importFrom(Biostrings,readAAStringSet)
+importFrom(Biostrings,readDNAMultipleAlignment)
 importFrom(Biostrings,toString)
 importFrom(Biostrings,unmasked)
 importFrom(RColorBrewer,brewer.pal)
diff --git a/R/CHANGED-pre-msa-tree.R b/R/CHANGED-pre-msa-tree.R
index 62fcdc5c..e9e9aac7 100644
--- a/R/CHANGED-pre-msa-tree.R
+++ b/R/CHANGED-pre-msa-tree.R
@@ -73,7 +73,9 @@ convert2TitleCase <- function(x, y = " ") {
 #' Default is 'pspa.txt'
 #' @param reduced Boolean. If TRUE, a reduced data frame will be generated with
 #' only one sequence per lineage. Default is FALSE.
+#' @param seq_type Character. Type of sequence, either "AA" or "DNA". Default is "AA".
 #'
+#' @importFrom Biostrings readAAMultipleAlignment readDNAMultipleAlignment
 #' @importFrom dplyr distinct left_join mutate select
 #' @importFrom purrr map
 #' @importFrom readr read_file read_tsv
@@ -99,7 +101,8 @@ convert2TitleCase <- function(x, y = " ") {
 addLeaves2Alignment <- function(aln_file = "",
     lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
     # lin_file="data/rawdata_tsv/PspA.txt",
-    reduced = FALSE) {
+    reduced = FALSE, 
+    seq_type = c("AA", "DNA")) {
     ## SAMPLE ARGS
     # aln_file <- "data/rawdata_aln/pspc.gismo.aln"
     # lin_file <- "data/rawdata_tsv/all_semiclean.txt"
@@ -108,25 +111,36 @@ addLeaves2Alignment <- function(aln_file = "",
     # 1. Read aln & lineage master files files w/ read_file/read_tsv
     # 2. paste and collapse files so they can be read w/ tsv
     # 3. If the file has 1 column, separate it
-    aln <- read_file(aln_file)
-    lin <- read_tsv(lin_file)
-    aln <- paste(aln, sep = "\\s+", collapse = "\\t")
-    aln <- read_tsv(aln, col_names = F)
-    if (length(aln) == 1) {
-        colnames(aln) <- "x1"
-        aln <- separate(aln,
-            col = .data$x1,
-            into = c("x1", "x2"),
-            sep = "\\s+"
-        )
-    }
+    seq_type <- match.arg(seq_type, c('AA', 'DNA'))
+
+    # Read lineage data
+    lin <- read_tsv(lin_file, show_col_types = FALSE)
 
-    colnames(aln) <- c("AccNum", "Alignment")
+    # Detect file format
+    first_line <- readLines(aln_file, n = 1)
+    is_clustal <- grepl("^CLUSTAL", first_line, ignore.case = TRUE)
 
+    if (is_clustal) {
+        rlang::inform(rlang::format_error_bullets(c("i" = "Detected Clustal alignment: using Biostrings parser")))
+        aln_obj <- switch(
+        seq_type,
+        AA = readAAMultipleAlignment(aln_file, format = "clustal"),
+        DNA = readDNAMultipleAlignment(aln_file, format = "clustal")
+        )
+
+        aln <- tibble(
+        AccNum = names(aln_obj),
+        Alignment = as.character(unmasked(aln_obj))
+        )
+    } else {
+        rlang::inform(rlang::format_error_bullets(c("i" = "Detected tabular alignment: reading with readr")))
+        aln <- read_tsv(aln_file, col_names = c("AccNum", "Alignment"), show_col_types = FALSE)
+    }
+    
     aln_lin <- left_join(aln, lin, by = "AccNum") %>%
         select(
-            .data$AccNum, .data$Alignment,
-            .data$Species, .data$Lineage
+            'AccNum', 'Alignment',
+            'Species', 'Lineage'
         )
 
     # Removes rows with NA
@@ -178,7 +192,7 @@ addLeaves2Alignment <- function(aln_file = "",
     # Create Leaf_AccNum pasted together
     # 2 columns Leaf_AccNum and Sequence Far left
     leaf_aln <- temp %>%
-        select(.data$Leaf_Acc, .data$Alignment)
+        select('Leaf_Acc', 'Alignment')
     return(leaf_aln)
 }
 
@@ -223,7 +237,9 @@ addName <- function(data,
     split_data <- data %>%
         separate(
             col = lin_col, into = c("Kingdom", "Phylum"),
-            sep = lin_sep
+            sep = lin_sep,
+            extra = 'drop',
+            fill = 'right'
         ) %>%
         mutate(
             Kingdom = strtrim(.data$Kingdom, 1),
@@ -302,10 +318,30 @@ addName <- function(data,
 #' addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
 #' }
 #'
+#' @importFrom data.table data.table
 convertAlignment2FA <- function(aln_file = "",
     lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
     fa_outpath = "",
     reduced = FALSE) {
+    # Check if the alignment file is provided and exists
+    if (nchar(aln_file) == 0) {
+        abort("Error: Alignment file path must be provided.")
+    }
+
+    if (!file.exists(aln_file)) {
+        abort(paste("Error: The alignment file '", aln_file, "' does not exist."))
+    }
+
+    # Check if the lineage file exists
+    if (!file.exists(lin_file)) {
+        abort(paste("Error: The lineage file '", lin_file, "' does not exist."))
+    }
+
+    # Check that the 'reduced' parameter is logical
+    if (!is.logical(reduced) || length(reduced) != 1) {
+        abort("Error: 'reduced' must be a single logical value (TRUE or FALSE).")
+    }
+
     ## SAMPLE ARGS
     # aln_file <- "data/rawdata_aln/pspc.gismo.aln"
     # lin_file <- "data/rawdata_tsv/all_semiclean.txt"
@@ -314,8 +350,8 @@ convertAlignment2FA <- function(aln_file = "",
 
     ## Add leaves
     aln <- addLeaves2Alignment(
-        aln = aln_file,
-        lin = lin_file,
+        aln_file = aln_file,
+        lin_file = lin_file,
         reduced = reduced
     )
     names <- aln$Leaf_Acc
@@ -451,12 +487,25 @@ renameFA <- function(fa_path, outpath,
 generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
     fa_outpath = here("data/alns/"),
     lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
-    reduced = F) {
-    # library(here)
-    # library(tidyverse)
-    # aln_path <- here("data/rawdata_aln/")
-    # outpath <- here("data/alns/")
-    # lin_file <- here("data/rawdata_tsv/all_semiclean.txt")
+    reduced = FALSE) {
+    
+    if (!dir.exists(aln_path)) {
+        abort("Error: The alignment directory does not exist at the specified
+             path: ", aln_path)
+    }
+
+    # Check if the output path exists; if not, attempt to create it
+    if (!dir.exists(fa_outpath)) {
+        dir.create(fa_outpath, recursive = TRUE)
+        message("Note: The output directory did not exist and has been created: ",
+                fa_outpath)
+    }
+
+    # Check if the lineage file exists
+    if (!file.exists(lin_file)) {
+        abort("Error: The lineage file does not exist at the specified path: ",
+             lin_file)
+    }
 
     aln_filenames <- list.files(path = aln_path, pattern = "*.aln")
     aln_filepaths <- paste0(aln_path, "/", aln_filenames)
@@ -726,7 +775,7 @@ writeMSA_AA2FA <- function(writeMSA_AA2FA, outpath) {
 #' }
 getAccNumFromFA <- function(fasta_file) {
     txt <- read_file(fasta_file)
-    accnums <- stringi::stri_extract_all_regex(fasta_file, "(?<=>)[\\w,.]+")[[1]]
+    accnums <- stringi::stri_extract_all_regex(txt, "(?<=>)[\\w,.]+")[[1]]
     return(accnums)
 }
 
diff --git a/R/pre-msa-tree.R b/R/pre-msa-tree.R
index 8cf3b8c3..3ad2478b 100644
--- a/R/pre-msa-tree.R
+++ b/R/pre-msa-tree.R
@@ -69,7 +69,7 @@ convert2TitleCase <- function(x, y = " ") {
 ################################
 ## Function to add leaves to an alignment file
 ## !! Add DA to leaves?
-#' addLeaves2Alignment
+#' addLeaves2Alignment_legacy
 #'
 #' @author Janani Ravi
 #'
@@ -109,7 +109,7 @@ convert2TitleCase <- function(x, y = " ") {
 #' \dontrun{
 #' addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
 #' }
-addLeaves2Alignment <- function(aln_file = "",
+addLeaves2Alignment_legacy <- function(aln_file = "",
     lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
     # lin_file="data/rawdata_tsv/PspA.txt",
     reduced = FALSE) {
@@ -243,7 +243,7 @@ addLeaves2Alignment <- function(aln_file = "",
 #' \dontrun{
 #' addName(data_frame)
 #' }
-addName <- function(data,
+addName_lecacy <- function(data,
     accnum_col = "AccNum", spec_col = "Species", lin_col = "Lineage",
     lin_sep = ">", out_col = "Name") {
     # Check if the data is a data fram
@@ -341,7 +341,7 @@ addName <- function(data,
 #' \dontrun{
 #' convertAlignment2FA("pspa_snf7.aln", "pspa.txt")
 #' }
-convertAlignment2FA <- function(aln_file = "",
+convertAlignment2FA_legacy <- function(aln_file = "",
     lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
     fa_outpath = "",
     reduced = FALSE) {
@@ -537,7 +537,7 @@ rename_fasta <- function(fa_path, outpath,
 #' \dontrun{
 #' generateAllAlignments2FA()
 #' }
-generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
+generateAllAlignments2FA_legacy <- function(aln_path = here("data/rawdata_aln/"),
     fa_outpath = here("data/alns/"),
     lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
     reduced = F) {
@@ -554,9 +554,9 @@ generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
                 fa_outpath)
     }
 
-    # Check if the linear file exists
+    # Check if the lineage file exists
     if (!file.exists(lin_file)) {
-        abort("Error: The linear file does not exist at the specified path: ",
+        abort("Error: The lineage file does not exist at the specified path: ",
              lin_file)
     }
     # library(here)
diff --git a/man/addLeaves2Alignment.Rd b/man/addLeaves2Alignment.Rd
index 85edc798..fa9849f3 100644
--- a/man/addLeaves2Alignment.Rd
+++ b/man/addLeaves2Alignment.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R
 \name{addLeaves2Alignment}
 \alias{addLeaves2Alignment}
 \title{addLeaves2Alignment}
@@ -7,17 +7,12 @@
 addLeaves2Alignment(
   aln_file = "",
   lin_file = "data/rawdata_tsv/all_semiclean.txt",
-  reduced = FALSE
-)
-
-addLeaves2Alignment(
-  aln_file = "",
-  lin_file = "data/rawdata_tsv/all_semiclean.txt",
-  reduced = FALSE
+  reduced = FALSE,
+  seq_type = c("AA", "DNA")
 )
 }
 \arguments{
-\item{aln_file}{Character. Path to file. Input tab-delimited file +
+\item{aln_file}{haracter. Path to file. Input tab-delimited file +
 alignment file accnum & alignment.
 Default is 'pspa_snf7.aln'}
 
@@ -27,34 +22,23 @@ Default is 'pspa.txt'}
 
 \item{reduced}{Boolean. If TRUE, a reduced data frame will be generated with
 only one sequence per lineage. Default is FALSE.}
+
+\item{seq_type}{Character. Type of sequence, either "AA" or "DNA". Default is "AA".}
 }
 \value{
 A data frame containing the enriched alignment data with lineage
 information.
-
-A data frame containing the combined alignment and lineage
-information.
 }
 \description{
-Adding Leaves to an alignment file w/ accessions
-Genomic Contexts vs Domain Architectures.
-
 Adding Leaves to an alignment file w/ accessions
 Genomic Contexts vs Domain Architectures.
 }
 \details{
-The alignment file would need two columns: 1. accession +
-number and 2. alignment. The protein homolog accession to lineage mapping +
-file should have
-
 The alignment file would need two columns: 1. accession +
 number and 2. alignment. The protein homolog accession to lineage mapping +
 file should have
 }
 \note{
-Please refer to the source code if you have alternate +
-file formats and/or column names.
-
 Please refer to the source code if you have alternate +
 file formats and/or column names.
 }
@@ -62,9 +46,6 @@ file formats and/or column names.
 \dontrun{
 addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
 }
-\dontrun{
-addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
-}
 }
 \author{
 Janani Ravi
diff --git a/man/addLeaves2Alignment_legacy.Rd b/man/addLeaves2Alignment_legacy.Rd
new file mode 100644
index 00000000..6e00e54b
--- /dev/null
+++ b/man/addLeaves2Alignment_legacy.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pre-msa-tree.R
+\name{addLeaves2Alignment_legacy}
+\alias{addLeaves2Alignment_legacy}
+\title{addLeaves2Alignment_legacy}
+\usage{
+addLeaves2Alignment_legacy(
+  aln_file = "",
+  lin_file = "data/rawdata_tsv/all_semiclean.txt",
+  reduced = FALSE
+)
+}
+\arguments{
+\item{aln_file}{Character. Path to file. Input tab-delimited file +
+alignment file accnum & alignment.
+Default is 'pspa_snf7.aln'}
+
+\item{lin_file}{Character. Path to file. Protein file with accession +
+number to lineage mapping.
+Default is 'pspa.txt'}
+
+\item{reduced}{Boolean. If TRUE, a reduced data frame will be generated with
+only one sequence per lineage. Default is FALSE.}
+}
+\value{
+A data frame containing the combined alignment and lineage
+information.
+}
+\description{
+Adding Leaves to an alignment file w/ accessions
+Genomic Contexts vs Domain Architectures.
+}
+\details{
+The alignment file would need two columns: 1. accession +
+number and 2. alignment. The protein homolog accession to lineage mapping +
+file should have
+}
+\note{
+Please refer to the source code if you have alternate +
+file formats and/or column names.
+}
+\examples{
+\dontrun{
+addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
+}
+}
+\author{
+Janani Ravi
+}
+\keyword{accnum,}
+\keyword{alignment,}
+\keyword{leaves,}
+\keyword{lineage,}
+\keyword{species}
diff --git a/man/addName.Rd b/man/addName.Rd
index b681f349..e8d511a2 100644
--- a/man/addName.Rd
+++ b/man/addName.Rd
@@ -1,18 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R
 \name{addName}
 \alias{addName}
 \title{addName}
 \usage{
-addName(
-  data,
-  accnum_col = "AccNum",
-  spec_col = "Species",
-  lin_col = "Lineage",
-  lin_sep = ">",
-  out_col = "Name"
-)
-
 addName(
   data,
   accnum_col = "AccNum",
@@ -37,16 +28,11 @@ addName(
 Lineage, and AccNum info}
 }
 \value{
-Original data with a 'Name' column
-
 Original data with a 'Name' column
 }
 \description{
 This function adds a new 'Name' column that is comprised of components from
 Kingdom, Phylum, Genus, and species, as well as the accession
-
-This function adds a new 'Name' column that is comprised of
-components from Kingdom, Phylum, Genus, and species, as well as the accession
 }
 \examples{
 # Example usage of the addName function
@@ -57,9 +43,6 @@ data <- data.frame(
 )
 enriched_data <- addName(data)
 enriched_data
-\dontrun{
-addName(data_frame)
-}
 }
 \author{
 Samuel Chen, Janani Ravi
diff --git a/man/addName_lecacy.Rd b/man/addName_lecacy.Rd
new file mode 100644
index 00000000..6dfeee44
--- /dev/null
+++ b/man/addName_lecacy.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pre-msa-tree.R
+\name{addName_lecacy}
+\alias{addName_lecacy}
+\title{addName}
+\usage{
+addName_lecacy(
+  data,
+  accnum_col = "AccNum",
+  spec_col = "Species",
+  lin_col = "Lineage",
+  lin_sep = ">",
+  out_col = "Name"
+)
+}
+\arguments{
+\item{data}{Data to add name column to}
+
+\item{accnum_col}{Column containing accession numbers}
+
+\item{spec_col}{Column containing species}
+
+\item{lin_col}{Column containing lineage}
+
+\item{lin_sep}{Character separating lineage levels}
+
+\item{out_col}{Column that contains the new 'Name' derived from Species,
+Lineage, and AccNum info}
+}
+\value{
+Original data with a 'Name' column
+}
+\description{
+This function adds a new 'Name' column that is comprised of
+components from Kingdom, Phylum, Genus, and species, as well as the accession
+}
+\examples{
+\dontrun{
+addName(data_frame)
+}
+}
+\author{
+Samuel Chen, Janani Ravi
+}
diff --git a/man/convertAlignment2FA.Rd b/man/convertAlignment2FA.Rd
index 528868c0..a776c943 100644
--- a/man/convertAlignment2FA.Rd
+++ b/man/convertAlignment2FA.Rd
@@ -1,16 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R
 \name{convertAlignment2FA}
 \alias{convertAlignment2FA}
 \title{convertAlignment2FA}
 \usage{
-convertAlignment2FA(
-  aln_file = "",
-  lin_file = "data/rawdata_tsv/all_semiclean.txt",
-  fa_outpath = "",
-  reduced = FALSE
-)
-
 convertAlignment2FA(
   aln_file = "",
   lin_file = "data/rawdata_tsv/all_semiclean.txt",
@@ -30,35 +23,24 @@ Default is 'pspa.txt'}
 \item{fa_outpath}{Character. Path to the written fasta file.
 Default is 'NULL'}
 
-\item{reduced}{Boolean. If TRUE, the fasta file will contain only one
-sequence per lineage. Default is 'FALSE'}
+\item{reduced}{Boolean. If TRUE, the fasta file will contain only one sequence per lineage.
+Default is 'FALSE'}
 }
 \value{
 A character string representing the FASTA formatted sequences.
 If \code{fa_outpath} is provided, the FASTA will also be saved to the specified
 file.
-
-Character string containing the Fasta formatted sequences.
-If \code{fa_outpath} is specified, the function also writes the sequences to the
-Fasta file.
 }
 \description{
 Adding Leaves to an alignment file w/ accessions
 Genomic Contexts vs Domain Architectures.
 }
 \details{
-The alignment file would need two columns: 1. accession +
-number and 2. alignment. The protein homolog accession to lineage mapping +
-file should have
-
 The alignment file would need two columns: 1. accession +
 number and 2. alignment. The protein homolog accession to lineage mapping +
 file should have
 }
 \note{
-Please refer to the source code if you have alternate +
-file formats and/or column names.
-
 Please refer to the source code if you have alternate +
 file formats and/or column names.
 }
@@ -67,9 +49,6 @@ file formats and/or column names.
 addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
 }
 
-\dontrun{
-convertAlignment2FA("pspa_snf7.aln", "pspa.txt")
-}
 }
 \author{
 Janani Ravi
diff --git a/man/convertAlignment2FA_legacy.Rd b/man/convertAlignment2FA_legacy.Rd
new file mode 100644
index 00000000..689a7071
--- /dev/null
+++ b/man/convertAlignment2FA_legacy.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pre-msa-tree.R
+\name{convertAlignment2FA_legacy}
+\alias{convertAlignment2FA_legacy}
+\title{convertAlignment2FA}
+\usage{
+convertAlignment2FA_legacy(
+  aln_file = "",
+  lin_file = "data/rawdata_tsv/all_semiclean.txt",
+  fa_outpath = "",
+  reduced = FALSE
+)
+}
+\arguments{
+\item{aln_file}{Character. Path to file. Input tab-delimited file +
+alignment file accnum & alignment.
+Default is 'pspa_snf7.aln'}
+
+\item{lin_file}{Character. Path to file. Protein file with accession +
+number to lineage mapping.
+Default is 'pspa.txt'}
+
+\item{fa_outpath}{Character. Path to the written fasta file.
+Default is 'NULL'}
+
+\item{reduced}{Boolean. If TRUE, the fasta file will contain only one
+sequence per lineage. Default is 'FALSE'}
+}
+\value{
+Character string containing the Fasta formatted sequences.
+If \code{fa_outpath} is specified, the function also writes the sequences to the
+Fasta file.
+}
+\description{
+convertAlignment2FA
+}
+\details{
+The alignment file would need two columns: 1. accession +
+number and 2. alignment. The protein homolog accession to lineage mapping +
+file should have
+}
+\note{
+Please refer to the source code if you have alternate +
+file formats and/or column names.
+}
+\examples{
+\dontrun{
+convertAlignment2FA("pspa_snf7.aln", "pspa.txt")
+}
+}
+\author{
+Janani Ravi
+}
+\keyword{accnum,}
+\keyword{alignment,}
+\keyword{leaves,}
+\keyword{lineage,}
+\keyword{species}
diff --git a/man/generateAllAlignments2FA.Rd b/man/generateAllAlignments2FA.Rd
index 421d8cf7..8cc11e4e 100644
--- a/man/generateAllAlignments2FA.Rd
+++ b/man/generateAllAlignments2FA.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R
 \name{generateAllAlignments2FA}
 \alias{generateAllAlignments2FA}
 \title{generateAllAlignments2FA}
@@ -8,14 +8,7 @@ generateAllAlignments2FA(
   aln_path = here("data/rawdata_aln/"),
   fa_outpath = here("data/alns/"),
   lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
-  reduced = F
-)
-
-generateAllAlignments2FA(
-  aln_path = here("data/rawdata_aln/"),
-  fa_outpath = here("data/alns/"),
-  lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
-  reduced = F
+  reduced = FALSE
 )
 }
 \arguments{
@@ -34,28 +27,15 @@ sequence per lineage.
 Default is 'FALSE'.}
 }
 \value{
-NULL. The function saves the output FASTA files to the specified
-directory.
-
 NULL. The function saves the output FASTA files to the specified
 directory.
 }
 \description{
 Adding Leaves to an alignment file w/ accessions
 
-Adding Leaves to all alignment files w/ accessions & DAs?
-
-Adding Leaves to an alignment file w/ accessions
-
 Adding Leaves to all alignment files w/ accessions & DAs?
 }
 \details{
-The alignment files would need two columns separated by spaces:
-\enumerate{
-\item AccNum and 2. alignment. The protein homolog file should have AccNum,
-Species, Lineages.
-}
-
 The alignment files would need two columns separated by spaces:
 \enumerate{
 \item AccNum and 2. alignment. The protein homolog file should have AccNum,
@@ -63,9 +43,6 @@ Species, Lineages.
 }
 }
 \note{
-Please refer to the source code if you have alternate + file formats
-and/or column names.
-
 Please refer to the source code if you have alternate + file formats
 and/or column names.
 }
@@ -73,9 +50,6 @@ and/or column names.
 \dontrun{
 generateAllAlignments2FA()
 }
-\dontrun{
-generateAllAlignments2FA()
-}
 }
 \keyword{accnum,}
 \keyword{alignment,}
diff --git a/man/generateAllAlignments2FA_legacy.Rd b/man/generateAllAlignments2FA_legacy.Rd
new file mode 100644
index 00000000..c8d3df6e
--- /dev/null
+++ b/man/generateAllAlignments2FA_legacy.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pre-msa-tree.R
+\name{generateAllAlignments2FA_legacy}
+\alias{generateAllAlignments2FA_legacy}
+\title{generateAllAlignments2FA}
+\usage{
+generateAllAlignments2FA_legacy(
+  aln_path = here("data/rawdata_aln/"),
+  fa_outpath = here("data/alns/"),
+  lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
+  reduced = F
+)
+}
+\arguments{
+\item{aln_path}{Character. Path to alignment files.
+Default is 'here("data/rawdata_aln/")'}
+
+\item{fa_outpath}{Character. Path to file. Master protein file with AccNum &
+lineages.
+Default is 'here("data/rawdata_tsv/all_semiclean.txt")'}
+
+\item{lin_file}{Character. Path to the written fasta file.
+Default is 'here("data/alns/")'.}
+
+\item{reduced}{Boolean. If TRUE, the fasta file will contain only one
+sequence per lineage.
+Default is 'FALSE'.}
+}
+\value{
+NULL. The function saves the output FASTA files to the specified
+directory.
+}
+\description{
+Adding Leaves to an alignment file w/ accessions
+
+Adding Leaves to all alignment files w/ accessions & DAs?
+}
+\details{
+The alignment files would need two columns separated by spaces:
+\enumerate{
+\item AccNum and 2. alignment. The protein homolog file should have AccNum,
+Species, Lineages.
+}
+}
+\note{
+Please refer to the source code if you have alternate + file formats
+and/or column names.
+}
+\examples{
+\dontrun{
+generateAllAlignments2FA()
+}
+}
+\keyword{accnum,}
+\keyword{alignment,}
+\keyword{leaves,}
+\keyword{lineage,}
+\keyword{species}
diff --git a/tests/testthat/test-CHANGED-pre-msa-tree.R b/tests/testthat/test-CHANGED-pre-msa-tree.R
new file mode 100644
index 00000000..1a466a80
--- /dev/null
+++ b/tests/testthat/test-CHANGED-pre-msa-tree.R
@@ -0,0 +1,525 @@
+context("CHANGED-test-pre-msa-tree")
+test_that("CHANGED-test-pre-msa-tree", {
+    # Test with standard input
+    expect_equal(convert2TitleCase("hello world"), "Hello World")
+    expect_equal(convert2TitleCase("this is a test"), "This Is A Test")
+    
+    # Test with single word
+    expect_equal(convert2TitleCase("R"), "R")
+    expect_equal(convert2TitleCase("hello"), "Hello")
+    
+    # Test with punctuation
+    expect_equal(convert2TitleCase("capitalize every word."), 
+                 "Capitalize Every Word.")
+    expect_equal(convert2TitleCase("test, case, example"), 
+                 "Test, Case, Example")
+    
+    # Test with empty string
+    expect_equal(convert2TitleCase(""), "")
+    
+    # Test with multiple spaces
+    expect_equal(convert2TitleCase("  multiple   spaces  "), 
+                 "  Multiple   Spaces ")
+    
+    # Create mock alignment data
+    mock_alignment_data <- c(
+        "ACU53894.1\tMKTIIALSYI",
+        "APJ14606.1\tGSLKVSISY",
+        "ABK37082.1\tMKTLVAILA"
+    )
+    
+    # Write the mock alignment data to a .aln file
+    aln_file <- file.path(tempdir(), "mock_alignment.aln")
+    writeLines(mock_alignment_data, aln_file)
+    
+    # Create mock lineage data
+    mock_lineage_data <- data.frame(
+        AccNum = c("ACU53894.1", "APJ14606.1", "ABK37082.1"),
+        Species = c("Species1", "Species2", "Species3"),
+        Lineage = c("Kingdom>Phylum1", "Kingdom>Phylum2", "Kingdom>Phylum3"),
+        stringsAsFactors = FALSE
+    )
+    
+    # Write lineage data to a TSV file
+    lin_file <- file.path(tempdir(), "mock_lineage.tsv")
+    write_tsv(mock_lineage_data, lin_file)
+    
+    # Now you can test the function
+    result <- addLeaves2Alignment(aln_file, lin_file, seq_type = 'AA')
+    
+    # Check the structure of the result
+    expect_is(result, "data.frame")
+    
+    # Check the columns in the result
+    expect_true("Leaf_Acc" %in% colnames(result))
+    expect_true("Alignment" %in% colnames(result))
+    
+    # Check the content of the Leaf_Acc column
+    expect_equal(result$Leaf_Acc[1], "KPhylum_NASpe_ACU53894.1") 
+    expect_equal(result$Leaf_Acc[2], "KPhylum_NASpe_APJ14606.1")   
+    expect_equal(result$Leaf_Acc[3], "KPhylum_NASpe_ABK37082.1") 
+    
+    # Check alignment sequences correspond to accession numbers
+    expect_equal(result$Alignment[1], "MKTIIALSYI")
+    expect_equal(result$Alignment[2], "GSLKVSISY")
+    expect_equal(result$Alignment[3], "MKTLVAILA")
+    
+    # Mock data to simulate input
+    mock_data <- tibble::tibble(
+        AccNum = c("Acc1", "Acc2", "Acc3", "Acc4"),
+        Species = c("Homo sapiens", "Escherichia coli", "Mus musculus", NA),
+        Lineage = c("Eukaryota>Chordata", "Bacteria>Proteobacteria", 
+                    "Eukaryota>Chordata", "Bacteria>Firmicutes")
+    )
+    result <- addName(mock_data)
+    
+    # Check that the output contains the new Name column
+    expect_true("Name" %in% colnames(result))
+    
+    # Check if the names are formatted correctly
+    expected_names <- c("EChorda_Hsapiens_Acc1", "BProteo_Ecoli_Acc2", 
+                        "EChorda_Mmusculus_Acc3", "BFirmic_Acc4")
+    expect_equal(result$Name, expected_names)
+    
+    # Test with NULL species column
+    result <- addName(mock_data, spec_col = NULL)
+    
+    # Check that species is ignored, and names are based on lineage and AccNum
+    expected_names <- c("EChorda_Acc1", "BProteo_Acc2",
+                        "EChorda_Acc3", "BFirmic_Acc4")
+    expect_equal(result$Name, expected_names)
+    
+    # Create mock data with missing values
+    mock_data_with_missing <- tibble::tibble(
+        AccNum = c("Acc1", "Acc2", "Acc3"),
+        Species = c(NA, "Escherichia coli", NA),
+        Lineage = c(NA, "Bacteria>Proteobacteria", "Eukaryota>Chordata")
+    )
+    
+    result <- addName(mock_data_with_missing)
+    
+    # Check that missing species and lineage data are handled correctly
+    expected_names <- c("_Acc1", "BProteo_Ecoli_Acc2", "EChorda_Acc3")
+    expect_equal(result$Name, expected_names)
+    
+    # Test with a different separator (e.g., "/")
+    mock_data_custom_sep <- mock_data
+    mock_data_custom_sep$Lineage <- gsub(">", "/", mock_data_custom_sep$Lineage)
+    
+    result <- addName(mock_data_custom_sep, lin_sep = "/")
+    
+    # Ensure the function correctly parses the lineage with the custom separator
+    expected_names <- c("EChorda_Hsapiens_Acc1", 
+                        "BProteo_Ecoli_Acc2", 
+                        "EChorda_Mmusculus_Acc3", 
+                        "BFirmic_Acc4")
+    expect_equal(result$Name, expected_names)
+    
+    # Test with an empty dataframe
+    empty_data <- tibble::tibble(AccNum = character(0), 
+                                 Species = character(0), 
+                                 Lineage = character(0))
+    
+    result <- addName(empty_data)
+    
+    # Ensure the result is still a dataframe with the expected structure
+    expect_equal(nrow(result), 0)
+    expect_true("Name" %in% colnames(result))
+    
+    # Create mock data that might result in extra underscores
+    mock_data_with_gaps <- tibble::tibble(
+        AccNum = c("Acc1", "Acc2"),
+        Species = c(NA, "Escherichia coli"),
+        Lineage = c("Eukaryota", "Bacteria>Proteobacteria")
+    )
+    
+    result <- addName(mock_data_with_gaps)
+    
+    # Ensure no extra underscores are present in the Name column
+    expected_names <- c("E_Acc1", "BProteo_Ecoli_Acc2")
+    expect_equal(result$Name, expected_names)
+    
+
+
+    
+    # Call the function to convert alignment to FASTA
+    result <- convertAlignment2FA(
+        aln_file = aln_file,
+        lin_file = lin_file,
+        fa_outpath = NULL,
+        reduced = FALSE
+    )
+    
+    # Expected FASTA format output
+    expected_fasta <- ">KPhylum_NASpe_ACU53894.1\nMKTIIALSYI\n>KPhylum_NASpe_APJ14606.1\nGSLKVSISY\n>KPhylum_NASpe_ABK37082.1\nMKTLVAILA\n"
+    
+    # Check if the result matches the expected FASTA output
+    expect_equal(result, expected_fasta)
+    
+    # Temporary output file path
+    fa_outpath <- tempfile(fileext = ".fasta")
+    
+    # Call the function to convert alignment to FASTA and save it to a file
+    convertAlignment2FA(
+        aln_file = aln_file,
+        lin_file = lin_file,
+        fa_outpath = fa_outpath,
+        reduced = FALSE
+    )
+    
+    # Read the generated FASTA file
+    fasta_content <- read_file(fa_outpath)
+    
+    # Expected FASTA format output
+    expected_fasta <- ">KPhylum_NASpe_ACU53894.1\nMKTIIALSYI\n>KPhylum_NASpe_APJ14606.1\nGSLKVSISY\n>KPhylum_NASpe_ABK37082.1\nMKTLVAILA\n"
+    
+    # Check if the generated file content matches the expected FASTA output
+    expect_equal(fasta_content, expected_fasta)
+    
+    # Call the function with reduced mode enabled
+    result <- convertAlignment2FA(
+        aln_file = aln_file,
+        lin_file = lin_file,
+        fa_outpath = NULL,
+        reduced = TRUE
+    )
+    
+    # In reduced mode, we expect one sequence per unique lineage
+    expected_fasta <- ">KPhylum_NASpe_ACU53894.1\nMKTIIALSYI\n>KPhylum_NASpe_APJ14606.1\nGSLKVSISY\n>KPhylum_NASpe_ABK37082.1\nMKTLVAILA\n"
+    
+    # Check if the result matches the expected FASTA output with 
+    # reduced sequences
+    expect_equal(result, expected_fasta)
+    
+    # Clean up mock files after test
+    file.remove(aln_file)
+    file.remove(lin_file)
+    
+    # Mock data for acc2name
+    acc2name <- tibble::tibble(
+        AccNum = c("Acc1", "Acc2", "Acc3", "Acc4"),
+        Name = c("Name1", "Name2", "Name3", "Name4")
+    )
+    
+    # Sample FASTA line with Acc1
+    line <- ">Acc1 AAAATTTTCCCCGGGG"
+    
+    # Call the function
+    result <- mapAcc2Name(line, acc2name)
+    
+    # Expected output
+    expected <- ">Name1"
+    
+    # Check if the result matches the expected output
+    expect_equal(result, expected)
+    
+    # Sample FASTA line with an unknown accession number
+    line <- ">Acc5 TTTTCCCCGGGGAAAA"
+    
+    # Call the function
+    result <- mapAcc2Name(line, acc2name)
+    
+    # Expected output (no match found)
+    expected <- ">NA"
+    
+    # Check if the result matches the expected output
+    expect_equal(result, expected)
+    
+    # Empty line
+    line <- ""
+    
+    # Call the function
+    result <- mapAcc2Name(line, acc2name)
+    
+    # Expected output (should return an empty or NA-like result)
+    expect_equal(result, ">NA")
+    
+    # Sample FASTA line with extra spaces
+    line <- ">Acc2    TTTTCCCCGGGGAAAA"
+    
+    # Call the function
+    result <- mapAcc2Name(line, acc2name)
+    
+    # Expected output
+    expected <- ">Name2"
+    
+    # Check if the result matches the expected output
+    expect_equal(result, expected)
+    
+    # Sample FASTA line with a lowercase accession number
+    # Acc1 is in lowercase, but acc2name has uppercase
+    line <- ">acc1 AAAATTTTCCCCGGGG"  
+    
+    # Call the function
+    result <- mapAcc2Name(line, acc2name)
+    
+    # Expected output: should not find the accession number 
+    # because of case difference
+    expected <- ">NA"
+    
+    # Check if the result matches the expected output
+    expect_equal(result, expected)
+    
+    # Mock data for acc2name
+    acc2name <- tibble::tibble(
+        AccNum = c("Acc1", "Acc2", "Acc3"),
+        Name = c("Name1", "Name2", "Name3")
+    )
+    
+    # Mock FASTA file lines
+    mock_fasta <- c(
+        ">Acc1 description",
+        "AAAATTTTCCCCGGGG",
+        ">Acc2 description",
+        "GGGGTTTTAAAACCCC",
+        ">Acc3 description",
+        "CCCCAAAAGGGGTTTT"
+    )
+    
+    # Create a temporary file for the mock FASTA file
+    fa_path <- tempfile(fileext = ".fa")
+    writeLines(mock_fasta, fa_path)
+    
+    # Output file path
+    outpath <- tempfile(fileext = ".fa")
+    
+    # Call the renameFA function
+    result <- renameFA(fa_path, outpath, 
+                       replacement_function = mapAcc2Name, 
+                       acc2name = acc2name)
+    
+    # Expected result after renaming
+    expected <- c(
+        ">Name1",
+        "AAAATTTTCCCCGGGG",
+        ">Name2",
+        "GGGGTTTTAAAACCCC",
+        ">Name3",
+        "CCCCAAAAGGGGTTTT"
+    )
+    
+    # Check if the result matches the expected output
+    expect_equal(result, expected)
+    
+    # Call the renameFA function
+    result <- renameFA(fa_path, outpath, 
+                       replacement_function = mapAcc2Name, 
+                       acc2name = acc2name)
+    
+    # Extract the sequence lines (should not change)
+    sequence_lines <- result[c(2, 4, 6)]
+    expected_sequences <- c("AAAATTTTCCCCGGGG", 
+                            "GGGGTTTTAAAACCCC", 
+                            "CCCCAAAAGGGGTTTT")
+    
+    # Check if sequence lines match the original content
+    expect_equal(sequence_lines, expected_sequences)
+    
+    # Custom function that just appends '_custom' to the accession number
+    custom_replacement <- function(line, ...) {
+        acc <- str_sub(line, 2) # Remove '>'
+        return(paste0(">", acc, "_custom"))
+    }
+    
+    # Call the renameFA function with the custom function
+    result <- renameFA(fa_path, outpath, 
+                       replacement_function = custom_replacement)
+    
+    # Expected result after renaming with the custom function
+    expected <- c(
+        ">Acc1 description_custom",
+        "AAAATTTTCCCCGGGG",
+        ">Acc2 description_custom",
+        "GGGGTTTTAAAACCCC",
+        ">Acc3 description_custom",
+        "CCCCAAAAGGGGTTTT"
+    )
+    
+    # Check if the result matches the expected output
+    expect_equal(result, expected)
+    
+    # Create an empty file
+    empty_fa <- tempfile(fileext = ".fa")
+    writeLines(character(0), empty_fa)
+    
+    # Call the renameFA function with the empty file
+    result <- renameFA(empty_fa, outpath, 
+                       replacement_function = mapAcc2Name, 
+                       acc2name = acc2name)
+    
+    # Expected output is an empty character vector
+    expect_equal(result, NULL)
+    
+    # Call the renameFA function with multiple sequences
+    result <- renameFA(fa_path, outpath, 
+                       replacement_function = mapAcc2Name, 
+                       acc2name = acc2name)
+    
+    # Expected result
+    expected <- c(
+        ">Name1",
+        "AAAATTTTCCCCGGGG",
+        ">Name2",
+        "GGGGTTTTAAAACCCC",
+        ">Name3",
+        "CCCCAAAAGGGGTTTT"
+    )
+    
+    # Check if the result matches the expected output
+    expect_equal(result, expected)
+    
+    # Setup: Create a temporary directory for alignment files
+    aln_dir <- tempdir()
+    fa_dir <- tempdir()
+    lin_dir <- tempdir()
+    
+    # Create tabular alignment files (two columns: AccNum <TAB> Alignment)
+    aln1 <- 
+      tibble::tibble(
+        AccNum = c("Acc1", "Acc2"),
+        Alignment = c("ATGCNNNN", "ATGCNNNN")
+        )
+
+    aln2 <- 
+      tibble::tibble(
+        AccNum = c("Acc3", "Acc4"),
+        Alignment = c("ATGCNNNN", "ATGCNNNN")
+        )
+
+    # Write without column names so read_tsv(..., col_names = c("AccNum","Alignment")) works
+    readr::write_tsv(aln1, file.path(aln_dir, "test1.aln"), col_names = FALSE)
+    readr::write_tsv(aln2, file.path(aln_dir, "test2.aln"), col_names = FALSE)
+    
+    # Create mock lineage data (AccNum, Species, Lineage)
+    mock_lineage_data <- tibble::tibble(
+        AccNum = c("Acc1", "Acc2", "Acc3", "Acc4"),
+        Species = c("Species A", "Species B", "Species C", "Species D"),
+        Lineage = c("Kingdom>Phylum1", "Kingdom>Phylum1", 
+                    "Kingdom>Phylum2", "Kingdom>Phylum2")
+    )
+    
+    # Save the mock lineage data as a TSV file
+    write_tsv(mock_lineage_data, file.path(lin_dir, "all_semiclean.txt"))
+    
+    # Call the function
+    generateAllAlignments2FA(aln_path = aln_dir, 
+                             fa_outpath = fa_dir, 
+                             lin_file = file.path(lin_dir, "all_semiclean.txt"))
+    
+    # Check if output files are created
+    output_files <- list.files(fa_dir, pattern = "*.fa", full.names = TRUE)
+    expect_true(length(output_files) > 0)
+    
+    # Create a temporary empty directory and test for error handling
+    empty_dir <- tempdir()
+    fa_dir <- tempdir()
+
+    # Setup: Create a temporary directory for alignment files
+    aln_dir <- tempdir()
+    fa_dir <- tempdir()
+    
+  # Create mock alignment data as a tibble
+    mock_aln <- tibble(
+        AccNum    = c("Acc1", "Acc2"),
+        Alignment = c("ATGCNNNN", "ATGCNNNN")
+    )
+
+    # Write as a tab-delimited file without header row
+    # (so read_tsv(..., col_names = c("AccNum","Alignment")) will work correctly)
+    write_tsv(mock_aln,
+            file = file.path(aln_dir, "test1.aln"),
+            col_names = FALSE)
+    # # Create mock alignment files
+    # writeLines(c(">Acc1\nATGCNNNN\n>Acc2\nATGCNNNN\n"), 
+    #            file.path(aln_dir, "test1.aln"))
+    
+    # Create mock lineage data
+    mock_lineage_data <- tibble::tibble(
+        AccNum = c("Acc1", "Acc2"),
+        Species = c("Species A", "Species B"),
+        Lineage = c("Kingdom>Phylum1", "Kingdom>Phylum1")
+    )
+    
+    # Save the mock lineage data as a TSV file
+    write_tsv(mock_lineage_data, file.path(lin_dir, "all_semiclean.txt"))
+    
+    # Call the function with reduced = TRUE
+    generateAllAlignments2FA(aln_path = aln_dir, 
+                             fa_outpath = fa_dir, 
+                             lin_file = file.path(lin_dir, "all_semiclean.txt"), 
+                             reduced = TRUE)
+    
+    # Check if output files are created
+    output_files <- list.files(fa_dir, pattern = "*.fa", full.names = TRUE)
+    expect_true(length(output_files) > 0)
+    
+    # Check the content of the output file
+    fasta_content <- readLines(outpath)
+    expect_equal(fasta_content[1], ">Name1")
+    
+    # Sample Data for Testing
+    prot_data <- tibble::tibble(
+        AccNum = c("A001", "A002", "A003", "A004", "A005"),
+        Lineage = c("L1", "L1", "L2", "L2", NA)
+    )
+    
+    result <- createRepresentativeAccNum(prot_data, reduced = "Lineage", accnum_col = "AccNum")
+    
+    expect_equal(result, c("A001", "A003"))  # A001 for L1 and A003 for L2
+    
+    result <- createRepresentativeAccNum(prot_data, reduced = "Lineage", accnum_col = "AccNum")
+    
+    expect_false(any(is.na(result)))  # No NA values in result
+    expect_equal(length(result), 2)    # Still only 2 unique Lineages
+    
+    prot_data_with_duplicates <- tibble::tibble(
+        AccNum = c("A001", "A001", "A002", "A003", "A004", "A004"),
+        Lineage = c("L1", "L1", "L2", "L2", "L3", "L3")
+    )
+    
+    result <- createRepresentativeAccNum(prot_data_with_duplicates, 
+                                    reduced = "Lineage", accnum_col = "AccNum")
+    
+    # A001 for L1, A002 for L2, and one for L3
+    expect_equal(result, c("A001", "A002", "A004"))  
+    
+    empty_data <- tibble::tibble(AccNum = character(), Lineage = character())
+    
+    result <- createRepresentativeAccNum(empty_data, 
+                                    reduced = "Lineage", 
+                                    accnum_col = "AccNum")
+    
+    expect_equal(result, NULL)  # Expecting an empty character vector
+    
+    # Create a mock FASTA file for testing
+    create_mock_fasta <- function(file_path) {
+        seqs <- c(">seq1\nACGT\n>seq2\nACGT\n>seq3\nACGT")
+        writeLines(seqs, con = file_path)
+    }
+    
+    # Path for the mock FASTA file
+    mock_fasta_path <- "mock_sequences.fasta"
+    create_mock_fasta(mock_fasta_path)
+    
+    aligned <- alignFasta(mock_fasta_path, tool = "Muscle")
+    
+    # Check the class of the returned object
+    expect_s4_class(aligned, "MsaAAMultipleAlignment")
+    
+    aligned <- alignFasta(mock_fasta_path, tool = "ClustalO")
+    
+    # Check the class of the returned object
+    expect_s4_class(aligned, "MsaAAMultipleAlignment")
+    
+    aligned <- alignFasta(mock_fasta_path, tool = "ClustalW")
+    
+    # Check the class of the returned object
+    expect_s4_class(aligned, "MsaAAMultipleAlignment")
+    
+    # Expect error for non-existing file
+    expect_error(alignFasta("non_existing_file.fasta", tool = "Muscle"), 
+                 "Error: The FASTA file does not exist: ") 
+    
+    # Clean up mock fasta file after tests
+    file.remove(mock_fasta_path)
+})