diff --git a/NAMESPACE b/NAMESPACE
index cfaaf650..fe4c23d6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,7 +4,6 @@ export(BinaryDomainNetwork)
 export(GCA2Lineage)
 export(GenContextNetwork)
 export(IPG2Lineage)
-export(RepresentativeAccNums)
 export(acc2FA)
 export(acc2Lineage)
 export(acc2fa)
@@ -12,8 +11,6 @@ export(addLeaves2Alignment)
 export(addLineage)
 export(addName)
 export(addTaxID)
-export(add_leaves)
-export(add_name)
 export(advanced_opts2est_walltime)
 export(alignFasta)
 export(assign_job_queue)
@@ -31,11 +28,11 @@ export(convert2TitleCase)
 export(convertAlignment2FA)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
-export(convert_aln2fa)
 export(countByColumn)
 export(createFA2Tree)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+export(createRepresentativeAccNum)
 export(createWordCloud2Element)
 export(createWordCloudElement)
 export(create_lineage_lookup)
@@ -49,15 +46,13 @@ export(findParalogs)
 export(formatJobArgumentsHTML)
 export(gc_undirected_network)
 export(generateAllAlignments2FA)
-export(generate_all_aln2fa)
 export(generate_msa)
+export(getAccNumFromFA)
 export(getTopAccByLinDomArch)
-export(get_accnums_from_fasta_file)
 export(get_proc_medians)
 export(get_proc_weights)
 export(make_opts2procs)
 export(mapAcc2Name)
-export(map_acc2name)
 export(map_advanced_opts2procs)
 export(msa_pdf)
 export(plotIPR2Viz)
@@ -83,14 +78,14 @@ export(removeTails)
 export(renameFA)
 export(rename_fasta)
 export(replaceQuestionMarks)
-export(reveql)
-export(reverse_operon)
+export(reverseOperonSeq)
 export(run_deltablast)
 export(run_rpsblast)
 export(selectLongestDuplicate)
 export(sendJobStatusEmail)
 export(shortenLineage)
 export(sinkReset)
+export(straightenOperonSeq)
 export(summarizeByLineage)
 export(summarizeDomArch)
 export(summarizeDomArch_ByLineage)
@@ -98,11 +93,10 @@ export(summarizeGenContext)
 export(summarizeGenContext_ByDomArchLineage)
 export(summarizeGenContext_ByLineage)
 export(themeGenes2)
-export(to_titlecase)
 export(totalGenContextOrDomArchCounts)
 export(validateCountDF)
 export(wordcloud3)
-export(write.MsaAAMultipleAlignment)
+export(writeMSA_AA2FA)
 export(write_proc_medians_table)
 export(write_proc_medians_yml)
 importFrom(Biostrings,AAStringSet)
diff --git a/R/CHANGED-pre-msa-tree.R b/R/CHANGED-pre-msa-tree.R
index c4a97589..2f6c8a62 100644
--- a/R/CHANGED-pre-msa-tree.R
+++ b/R/CHANGED-pre-msa-tree.R
@@ -54,7 +54,7 @@ convert2TitleCase <- function(x, y = " ") {
 ################################
 ## Function to add leaves to an alignment file
 ## !! Add DA to leaves?
-#' Adding Leaves to an alignment file w/ accessions
+#' addLeaves2Alignment
 #'
 #' @author Janani Ravi
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -178,7 +178,7 @@ addLeaves2Alignment <- function(aln_file = "",
 }
 
 
-#' Add Name
+#' addName
 #'
 #' @author Samuel Chen, Janani Ravi
 #' @description This function adds a new 'Name' column that is comprised of components from
@@ -252,7 +252,7 @@ addName <- function(data,
 
 ################################
 ## Function to convert alignment 'aln' to fasta format for MSA + Tree
-#' Adding Leaves to an alignment file w/ accessions
+#' convertAlignment2FA
 #'
 #' @author Janani Ravi
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -320,6 +320,9 @@ convertAlignment2FA <- function(aln_file = "",
     return(fasta)
 }
 
+#' mapAcc2Name
+#' 
+#' @description
 #' Default renameFA() replacement function. Maps an accession number to its name
 #'
 #' @param line The line of a fasta file starting with '>'
@@ -382,6 +385,9 @@ renameFA <- function(fa_path, outpath,
 
 ################################
 ## generateAllAlignments2FA
+#' generateAllAlignments2FA
+#' 
+#' @description 
 #' Adding Leaves to an alignment file w/ accessions
 #'
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -441,10 +447,11 @@ generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
 
 # accessions <- c("P12345","Q9UHC1","O15530","Q14624","P0DTD1")
 # accessions <- rep("ANY95992.1", 201)
-#' acc2FA converts protein accession numbers to a fasta format.
+#' acc2FA 
 #'
 #' @description
-#' Resulting fasta file is written to the outpath.
+#' converts protein accession numbers to a fasta format. Resulting 
+#' fasta file is written to the outpath.
 #'
 #' @author Samuel Chen, Janani Ravi
 #' @keywords accnum, fasta
@@ -539,6 +546,9 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
     return(result)
 }
 
+#' createRepresentativeAccNum
+#' 
+#' @description
 #' Function to generate a vector of one Accession number per distinct observation from 'reduced' column
 #'
 #' @author Samuel Chen, Janani Ravi
@@ -556,7 +566,7 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
 #' @export
 #'
 #' @examples
-RepresentativeAccNums <- function(prot_data,
+createRepresentativeAccNum <- function(prot_data,
     reduced = "Lineage",
     accnum_col = "AccNum") {
     # Get Unique reduced column and then bind the AccNums back to get one AccNum per reduced column
@@ -585,6 +595,9 @@ RepresentativeAccNums <- function(prot_data,
     return(accessions)
 }
 
+#' alignFasta
+#' 
+#' @description
 #' Perform a Multiple Sequence Alignment on a FASTA file.
 #'
 #' @author Samuel Chen, Janani Ravi
@@ -610,12 +623,12 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
     )
 
     if (typeof(outpath) == "character") {
-        write.MsaAAMultipleAlignment(aligned, outpath)
+        writeMSA_AA2FA(aligned, outpath)
     }
     return(aligned)
 }
 
-#' Write MsaAAMultpleAlignment Objects as algined fasta sequence
+#' writeMSA_AA2FA
 #'
 #' @description
 #' MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
@@ -632,7 +645,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
 #' @export
 #'
 #' @examples
-write.MsaAAMultipleAlignment <- function(alignment, outpath) {
+writeMSA_AA2FA <- function(alignment, outpath) {
     l <- length(rownames(alignment))
     fasta <- ""
     for (i in 1:l)
@@ -645,7 +658,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
     return(fasta)
 }
 
-#' Get accnums from fasta file
+#' getAccNumFromFA
 #'
 #' @param fasta_file
 #'
@@ -655,7 +668,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
 #' @export
 #'
 #' @examples
-get_accnums_from_fasta_file <- function(fasta_file) {
+getAccNumFromFA <- function(fasta_file) {
     txt <- read_file(fasta_file)
     accnums <- stringi::stri_extract_all_regex(fasta_file, "(?<=>)[\\w,.]+")[[1]]
     return(accnums)
diff --git a/R/pre-msa-tree.R b/R/pre-msa-tree.R
index 44979c3c..290a1644 100644
--- a/R/pre-msa-tree.R
+++ b/R/pre-msa-tree.R
@@ -49,7 +49,7 @@ api_key <- Sys.getenv("ENTREZ_API_KEY", unset = "YOUR_KEY_HERE")
 #' @export
 #'
 #' @examples
-to_titlecase <- function(x, y = " ") {
+convert2TitleCase <- function(x, y = " ") {
     s <- strsplit(x, y)[[1]]
     paste(toupper(substring(s, 1, 1)), substring(s, 2),
         sep = "", collapse = y
@@ -59,7 +59,7 @@ to_titlecase <- function(x, y = " ") {
 ################################
 ## Function to add leaves to an alignment file
 ## !! Add DA to leaves?
-#' Adding Leaves to an alignment file w/ accessions
+#' addLeaves2Alignment
 #'
 #' @author Janani Ravi
 #'
@@ -95,9 +95,9 @@ to_titlecase <- function(x, y = " ") {
 #'
 #' @examples
 #' \dontrun{
-#' add_leaves("pspa_snf7.aln", "pspa.txt")
+#' addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
 #' }
-add_leaves <- function(aln_file = "",
+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) {
@@ -184,7 +184,7 @@ add_leaves <- function(aln_file = "",
 }
 
 
-#' Title
+#' addName
 #'
 #' @author Samuel Chen, Janani Ravi
 #'
@@ -209,7 +209,7 @@ add_leaves <- function(aln_file = "",
 #' @export
 #'
 #' @examples
-add_name <- function(data,
+addName <- function(data,
     accnum_col = "AccNum", spec_col = "Species", lin_col = "Lineage",
     lin_sep = ">", out_col = "Name") {
     cols <- c(accnum_col, "Kingdom", "Phylum", "Genus", "Spp")
@@ -258,7 +258,7 @@ add_name <- function(data,
 
 ################################
 ## Function to convert alignment 'aln' to fasta format for MSA + Tree
-#' Adding Leaves to an alignment file w/ accessions
+#' convertAlignment2FA
 #'
 #' @author Janani Ravi
 #'
@@ -288,9 +288,9 @@ add_name <- function(data,
 #'
 #' @examples
 #' \dontrun{
-#' add_leaves("pspa_snf7.aln", "pspa.txt")
+#' convertAlignment2FA("pspa_snf7.aln", "pspa.txt")
 #' }
-convert_aln2fa <- function(aln_file = "",
+convertAlignment2FA <- function(aln_file = "",
     lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
     fa_outpath = "",
     reduced = FALSE) {
@@ -324,6 +324,9 @@ convert_aln2fa <- function(aln_file = "",
     return(fasta)
 }
 
+#' mapAcc2Name
+#' 
+#' @description
 #' Default rename_fasta() replacement function. Maps an accession number to its name
 #'
 #' @param line he line of a fasta file starting with '>'
@@ -340,7 +343,7 @@ convert_aln2fa <- function(aln_file = "",
 #' @export
 #'
 #' @examples
-map_acc2name <- function(line, acc2name, acc_col = "AccNum", name_col = "Name") {
+mapAcc2Name <- function(line, acc2name, acc_col = "AccNum", name_col = "Name") {
     # change to be the name equivalent to an add_names column
     # Find the first ' '
     end_acc <- str_locate(line, " ")[[1]]
@@ -386,7 +389,10 @@ rename_fasta <- function(fa_path, outpath,
 }
 
 ################################
-## generate_all_aln2fa
+## generateAllAlignments2FA
+#' generateAllAlignments2FA
+#' 
+#' @description
 #' Adding Leaves to an alignment file w/ accessions
 #'
 #' @author Janani Ravi
@@ -413,9 +419,9 @@ rename_fasta <- function(fa_path, outpath,
 #'
 #' @examples
 #' \dontrun{
-#' generate_all_aln2fa()
+#' generateAllAlignments2FA()
 #' }
-generate_all_aln2fa <- function(aln_path = here("data/rawdata_aln/"),
+generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
     fa_outpath = here("data/alns/"),
     lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
     reduced = F) {
@@ -448,6 +454,10 @@ generate_all_aln2fa <- function(aln_path = here("data/rawdata_aln/"),
 # accessions <- rep("ANY95992.1", 201)
 #' acc2fa
 #'
+#' @description
+#' converts protein accession numbers to a fasta format. Resulting 
+#' fasta file is written to the outpath.
+#' 
 #' @author Samuel Chen, Janani Ravi
 #' @keywords accnum, fasta
 #'
@@ -546,7 +556,7 @@ acc2fa <- function(accessions, outpath, plan = "sequential") {
     return(result)
 }
 
-#' RepresentativeAccNums
+#' createRepresentativeAccNum
 #'
 #' @description
 #' Function to generate a vector of one Accession number per distinct observation from 'reduced' column
@@ -566,7 +576,7 @@ acc2fa <- function(accessions, outpath, plan = "sequential") {
 #' @export
 #'
 #' @examples
-RepresentativeAccNums <- function(prot_data,
+createRepresentativeAccNum <- function(prot_data,
     reduced = "Lineage",
     accnum_col = "AccNum") {
     # Get Unique reduced column and then bind the AccNums back to get one AccNum per reduced column
@@ -623,15 +633,15 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
     )
 
     if (typeof(outpath) == "character") {
-        write.MsaAAMultipleAlignment(aligned, outpath)
+        writeMSA_AA2FA(aligned, outpath)
     }
     return(aligned)
 }
 
-#' write.MsaAAMultipleAlignment
+#' writeMSA_AA2FA
 #'
 #' @description
-#' Write MsaAAMultpleAlignment Objects as algined fasta sequence
+#' Write MsaAAMultpleAlignment Objects as aligned fasta sequence
 #' MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
 #' and msaMuscle from the 'msa' package
 #'
@@ -647,7 +657,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
 #' @export
 #'
 #' @examples
-write.MsaAAMultipleAlignment <- function(alignment, outpath) {
+writeMSA_AA2FA <- function(alignment, outpath) {
     l <- length(rownames(alignment))
     fasta <- ""
     for (i in 1:l)
@@ -660,7 +670,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
     return(fasta)
 }
 
-#' get_accnums_from_fasta_file
+#' getAccNumFromFA
 #'
 #' @param fasta_file
 #'
@@ -671,7 +681,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
 #' @export
 #'
 #' @examples
-get_accnums_from_fasta_file <- function(fasta_file) {
+getAccNumFromFA <- function(fasta_file) {
     txt <- read_file(fasta_file)
     accnums <- stringi::stri_extract_all_regex(fasta_file, "(?<=>)[\\w,.]+")[[1]]
     return(accnums)
diff --git a/R/reverse_operons.R b/R/reverse_operons.R
index e4bbd50e..a2570e8d 100755
--- a/R/reverse_operons.R
+++ b/R/reverse_operons.R
@@ -3,7 +3,7 @@
 # Modified by Janani Ravi and Samuel Chen
 
 
-#' reveql
+#' straightenOperonSeq
 #'
 #' @param prot
 #'
@@ -11,7 +11,7 @@
 #' @export
 #'
 #' @examples
-reveql <- function(prot) {
+straightenOperonSeq <- function(prot) {
     w <- prot # $GenContext.orig # was 'x'
 
     y <- rep(NA, length(w))
@@ -57,7 +57,7 @@ reveql <- function(prot) {
 
 ## The function to reverse operons
 
-#' reverse_operon
+#' reverseOperonSeq
 #'
 #' @param prot
 #'
@@ -65,7 +65,7 @@ reveql <- function(prot) {
 #' @export
 #'
 #' @examples
-reverse_operon <- function(prot) {
+reverseOperonSeq <- function(prot) {
     gencontext <- prot$GenContext
 
     gencontext <- gsub(pattern = ">", replacement = ">|", x = gencontext)
@@ -108,7 +108,7 @@ reverse_operon <- function(prot) {
 
 
 
-    ge <- lapply(1:length(ge), function(x) reveql(ge[[x]]))
+    ge <- lapply(1:length(ge), function(x) straightenOperonSeq(ge[[x]]))
 
     ye <- te[withouteq]
 
@@ -141,4 +141,4 @@ reverse_operon <- function(prot) {
 # colnames(prot) <- c("AccNum","GenContext.orig","len", "GeneName","TaxID","Species")
 
 ## ??? straighten operons
-# prot$GenContext.orig <- reverse_operon(prot)
+# prot$GenContext.orig <- reverseOperonSeq(prot)
diff --git a/man/acc2fa.Rd b/man/acc2fa.Rd
index 158b2d51..3e7a756d 100644
--- a/man/acc2fa.Rd
+++ b/man/acc2fa.Rd
@@ -15,6 +15,9 @@ Function may not work for vectors of length > 10,000}
 \item{plan}{}
 }
 \description{
+converts protein accession numbers to a fasta format. Resulting
+fasta file is written to the outpath.
+
 acc2fa converts protein accession numbers to a fasta format.
 Resulting fasta file is written to the outpath.
 }
diff --git a/man/addLeaves2Alignment.Rd b/man/addLeaves2Alignment.Rd
index a758ebd5..d00e6df7 100644
--- a/man/addLeaves2Alignment.Rd
+++ b/man/addLeaves2Alignment.Rd
@@ -1,9 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
 \name{addLeaves2Alignment}
 \alias{addLeaves2Alignment}
-\title{Adding Leaves to an alignment file w/ accessions}
+\title{addLeaves2Alignment}
 \usage{
+addLeaves2Alignment(
+  aln_file = "",
+  lin_file = "data/rawdata_tsv/all_semiclean.txt",
+  reduced = FALSE
+)
+
 addLeaves2Alignment(
   aln_file = "",
   lin_file = "data/rawdata_tsv/all_semiclean.txt",
@@ -11,7 +17,7 @@ addLeaves2Alignment(
 )
 }
 \arguments{
-\item{aln_file}{haracter. Path to file. Input tab-delimited file +
+\item{aln_file}{Character. Path to file. Input tab-delimited file +
 alignment file accnum & alignment.
 Default is 'pspa_snf7.aln'}
 
@@ -23,15 +29,25 @@ Default is 'pspa.txt'}
 only one sequence per lineage. Default is FALSE.}
 }
 \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.
 }
@@ -39,6 +55,9 @@ 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/addName.Rd b/man/addName.Rd
index e04f9849..6f171456 100644
--- a/man/addName.Rd
+++ b/man/addName.Rd
@@ -1,9 +1,18 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
 \name{addName}
 \alias{addName}
-\title{Add Name}
+\title{addName}
 \usage{
+addName(
+  data,
+  accnum_col = "AccNum",
+  spec_col = "Species",
+  lin_col = "Lineage",
+  lin_sep = ">",
+  out_col = "Name"
+)
+
 addName(
   data,
   accnum_col = "AccNum",
@@ -28,9 +37,14 @@ 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
 }
diff --git a/man/add_leaves.Rd b/man/add_leaves.Rd
deleted file mode 100644
index f1eeed10..00000000
--- a/man/add_leaves.Rd
+++ /dev/null
@@ -1,50 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pre-msa-tree.R
-\name{add_leaves}
-\alias{add_leaves}
-\title{Adding Leaves to an alignment file w/ accessions}
-\usage{
-add_leaves(
-  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.}
-}
-\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{
-add_leaves("pspa_snf7.aln", "pspa.txt")
-}
-}
-\author{
-Janani Ravi
-}
-\keyword{accnum,}
-\keyword{alignment,}
-\keyword{leaves,}
-\keyword{lineage,}
-\keyword{species}
diff --git a/man/add_name.Rd b/man/add_name.Rd
deleted file mode 100644
index f19139e1..00000000
--- a/man/add_name.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pre-msa-tree.R
-\name{add_name}
-\alias{add_name}
-\title{Title}
-\usage{
-add_name(
-  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
-}
-\author{
-Samuel Chen, Janani Ravi
-}
diff --git a/man/alignFasta.Rd b/man/alignFasta.Rd
index 21b020cf..02a3026b 100644
--- a/man/alignFasta.Rd
+++ b/man/alignFasta.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
 \name{alignFasta}
 \alias{alignFasta}
-\title{Perform a Multiple Sequence Alignment on a FASTA file.}
+\title{alignFasta}
 \usage{
 alignFasta(fasta_file, tool = "Muscle", outpath = NULL)
 
@@ -21,6 +21,8 @@ aligned fasta sequence as a MsaAAMultipleAlignment object
 aligned fasta sequence as a MsaAAMultipleAlignment object
 }
 \description{
+Perform a Multiple Sequence Alignment on a FASTA file.
+
 Perform a Multiple Sequence Alignment on a FASTA file.
 }
 \author{
diff --git a/man/convert2TitleCase.Rd b/man/convert2TitleCase.Rd
index 84e7fa00..72619285 100644
--- a/man/convert2TitleCase.Rd
+++ b/man/convert2TitleCase.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
 \name{convert2TitleCase}
 \alias{convert2TitleCase}
 \alias{totitle,}
@@ -7,6 +7,8 @@
 \title{Changing case to 'Title Case'}
 \usage{
 convert2TitleCase(text, delimitter)
+
+to_titlecase(text, delimitter)
 }
 \arguments{
 \item{x}{Character vector.}
@@ -15,8 +17,13 @@ convert2TitleCase(text, delimitter)
 }
 \description{
 Translate string to Title Case w/ delimitter.
+
+Translate string to Title Case w/ delimitter.
+Changing case to 'Title Case'
 }
 \seealso{
+chartr, toupper, and tolower.
+
 chartr, toupper, and tolower.
 }
 \author{
diff --git a/man/convertAlignment2FA.Rd b/man/convertAlignment2FA.Rd
index d6b4dc56..8e9ceb94 100644
--- a/man/convertAlignment2FA.Rd
+++ b/man/convertAlignment2FA.Rd
@@ -1,9 +1,16 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
 \name{convertAlignment2FA}
 \alias{convertAlignment2FA}
-\title{Adding Leaves to an alignment file w/ accessions}
+\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",
@@ -31,11 +38,18 @@ 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.
 }
@@ -44,6 +58,9 @@ 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/convert_aln2fa.Rd b/man/convert_aln2fa.Rd
deleted file mode 100644
index 8bebe31d..00000000
--- a/man/convert_aln2fa.Rd
+++ /dev/null
@@ -1,53 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pre-msa-tree.R
-\name{convert_aln2fa}
-\alias{convert_aln2fa}
-\title{Adding Leaves to an alignment file w/ accessions}
-\usage{
-convert_aln2fa(
-  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'}
-}
-\description{
-Adding Leaves to an alignment file w/ accessions
-}
-\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{
-add_leaves("pspa_snf7.aln", "pspa.txt")
-}
-}
-\author{
-Janani Ravi
-}
-\keyword{accnum,}
-\keyword{alignment,}
-\keyword{leaves,}
-\keyword{lineage,}
-\keyword{species}
diff --git a/man/RepresentativeAccNums.Rd b/man/createRepresentativeAccNum.Rd
similarity index 60%
rename from man/RepresentativeAccNums.Rd
rename to man/createRepresentativeAccNum.Rd
index f617cde4..3bd20522 100644
--- a/man/RepresentativeAccNums.Rd
+++ b/man/createRepresentativeAccNum.Rd
@@ -1,12 +1,20 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
-\name{RepresentativeAccNums}
-\alias{RepresentativeAccNums}
-\title{Function to generate a vector of one Accession number per distinct observation from 'reduced' column}
+\name{createRepresentativeAccNum}
+\alias{createRepresentativeAccNum}
+\title{createRepresentativeAccNum}
 \usage{
-RepresentativeAccNums(prot_data, reduced = "Lineage", accnum_col = "AccNum")
+createRepresentativeAccNum(
+  prot_data,
+  reduced = "Lineage",
+  accnum_col = "AccNum"
+)
 
-RepresentativeAccNums(prot_data, reduced = "Lineage", accnum_col = "AccNum")
+createRepresentativeAccNum(
+  prot_data,
+  reduced = "Lineage",
+  accnum_col = "AccNum"
+)
 }
 \arguments{
 \item{prot_data}{Data frame containing Accession Numbers}
@@ -18,6 +26,8 @@ One accession number will be assigned for each of these observations}
 \item{accnum_col}{Column from prot_data that contains Accession Numbers}
 }
 \description{
+Function to generate a vector of one Accession number per distinct observation from 'reduced' column
+
 Function to generate a vector of one Accession number per distinct observation from 'reduced' column
 }
 \author{
diff --git a/man/generateAllAlignments2FA.Rd b/man/generateAllAlignments2FA.Rd
index 3bf9938a..8f9d8ffc 100644
--- a/man/generateAllAlignments2FA.Rd
+++ b/man/generateAllAlignments2FA.Rd
@@ -1,9 +1,16 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
 \name{generateAllAlignments2FA}
 \alias{generateAllAlignments2FA}
-\title{Adding Leaves to an alignment file w/ accessions}
+\title{generateAllAlignments2FA}
 \usage{
+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/"),
@@ -15,28 +22,44 @@ generateAllAlignments2FA(
 \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.
+\item{fa_outpath}{Character. Path to the written fasta file.
 Default is 'here("data/alns/")'.}
 
+\item{lin_file}{Character. Path to file. Master protein file with AccNum & lineages.
+Default is 'here("data/rawdata_tsv/all_semiclean.txt")'}
+
 \item{reduced}{Boolean. If TRUE, the fasta file will contain only one sequence per lineage.
 Default is 'FALSE'.}
 }
 \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: 1. AccNum and 2. alignment. The protein homolog file should have AccNum, Species, Lineages.
+
 The alignment files would need two columns separated by spaces: 1. 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.
+
 Please refer to the source code if you have alternate + file formats and/or column names.
 }
 \examples{
 \dontrun{
 generateAllAlignments2FA()
 }
+\dontrun{
+generateAllAlignments2FA()
+}
+}
+\author{
+Janani Ravi
 }
 \keyword{accnum,}
 \keyword{alignment,}
diff --git a/man/generate_all_aln2fa.Rd b/man/generate_all_aln2fa.Rd
deleted file mode 100644
index ad6b7136..00000000
--- a/man/generate_all_aln2fa.Rd
+++ /dev/null
@@ -1,48 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pre-msa-tree.R
-\name{generate_all_aln2fa}
-\alias{generate_all_aln2fa}
-\title{Adding Leaves to an alignment file w/ accessions}
-\usage{
-generate_all_aln2fa(
-  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 the written fasta file.
-Default is 'here("data/alns/")'.}
-
-\item{lin_file}{Character. Path to file. Master protein file with AccNum & lineages.
-Default is 'here("data/rawdata_tsv/all_semiclean.txt")'}
-
-\item{reduced}{Boolean. If TRUE, the fasta file will contain only one sequence per lineage.
-Default is 'FALSE'.}
-}
-\description{
-Adding Leaves to all alignment files w/ accessions & DAs?
-}
-\details{
-The alignment files would need two columns separated by spaces: 1. 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{
-generate_all_aln2fa()
-}
-}
-\author{
-Janani Ravi
-}
-\keyword{accnum,}
-\keyword{alignment,}
-\keyword{leaves,}
-\keyword{lineage,}
-\keyword{species}
diff --git a/man/getAccNumFromFA.Rd b/man/getAccNumFromFA.Rd
new file mode 100644
index 00000000..d3ab8177
--- /dev/null
+++ b/man/getAccNumFromFA.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
+\name{getAccNumFromFA}
+\alias{getAccNumFromFA}
+\title{getAccNumFromFA}
+\usage{
+getAccNumFromFA(fasta_file)
+
+getAccNumFromFA(fasta_file)
+}
+\arguments{
+\item{fasta_file}{}
+}
+\description{
+getAccNumFromFA
+
+getAccNumFromFA
+}
diff --git a/man/get_accnums_from_fasta_file.Rd b/man/get_accnums_from_fasta_file.Rd
deleted file mode 100644
index 84c163cc..00000000
--- a/man/get_accnums_from_fasta_file.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
-\name{get_accnums_from_fasta_file}
-\alias{get_accnums_from_fasta_file}
-\title{Get accnums from fasta file}
-\usage{
-get_accnums_from_fasta_file(fasta_file)
-
-get_accnums_from_fasta_file(fasta_file)
-}
-\arguments{
-\item{fasta_file}{}
-}
-\description{
-Get accnums from fasta file
-
-get_accnums_from_fasta_file
-}
diff --git a/man/mapAcc2Name.Rd b/man/mapAcc2Name.Rd
index 0f5d447d..39ecb065 100644
--- a/man/mapAcc2Name.Rd
+++ b/man/mapAcc2Name.Rd
@@ -1,13 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CHANGED-pre-msa-tree.R
+% Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
 \name{mapAcc2Name}
 \alias{mapAcc2Name}
-\title{Default renameFA() replacement function. Maps an accession number to its name}
+\title{mapAcc2Name}
 \usage{
+mapAcc2Name(line, acc2name, acc_col = "AccNum", name_col = "Name")
+
 mapAcc2Name(line, acc2name, acc_col = "AccNum", name_col = "Name")
 }
 \arguments{
-\item{line}{The line of a fasta file starting with '>'}
+\item{line}{he line of a fasta file starting with '>'}
 
 \item{acc2name}{Data Table containing a column of accession numbers and a name column}
 
@@ -18,4 +20,6 @@ are mapped to}
 }
 \description{
 Default renameFA() replacement function. Maps an accession number to its name
+
+Default rename_fasta() replacement function. Maps an accession number to its name
 }
diff --git a/man/map_acc2name.Rd b/man/map_acc2name.Rd
deleted file mode 100644
index fcdb3023..00000000
--- a/man/map_acc2name.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pre-msa-tree.R
-\name{map_acc2name}
-\alias{map_acc2name}
-\title{Default rename_fasta() replacement function. Maps an accession number to its name}
-\usage{
-map_acc2name(line, acc2name, acc_col = "AccNum", name_col = "Name")
-}
-\arguments{
-\item{line}{he line of a fasta file starting with '>'}
-
-\item{acc2name}{Data Table containing a column of accession numbers and a name column}
-
-\item{acc_col}{Name of the column containing Accession numbers}
-
-\item{name_col}{Name of the column containing the names that the accession numbers
-are mapped to}
-}
-\description{
-Default rename_fasta() replacement function. Maps an accession number to its name
-}
diff --git a/man/reveql.Rd b/man/reverseOperonSeq.Rd
similarity index 56%
rename from man/reveql.Rd
rename to man/reverseOperonSeq.Rd
index 9dc2bcb8..d61ec5f2 100644
--- a/man/reveql.Rd
+++ b/man/reverseOperonSeq.Rd
@@ -1,14 +1,14 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/reverse_operons.R
-\name{reveql}
-\alias{reveql}
-\title{reveql}
+\name{reverseOperonSeq}
+\alias{reverseOperonSeq}
+\title{reverseOperonSeq}
 \usage{
-reveql(prot)
+reverseOperonSeq(prot)
 }
 \arguments{
 \item{prot}{}
 }
 \description{
-reveql
+reverseOperonSeq
 }
diff --git a/man/reverse_operon.Rd b/man/straightenOperonSeq.Rd
similarity index 53%
rename from man/reverse_operon.Rd
rename to man/straightenOperonSeq.Rd
index 270e2a62..fcd0c923 100644
--- a/man/reverse_operon.Rd
+++ b/man/straightenOperonSeq.Rd
@@ -1,14 +1,14 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/reverse_operons.R
-\name{reverse_operon}
-\alias{reverse_operon}
-\title{reverse_operon}
+\name{straightenOperonSeq}
+\alias{straightenOperonSeq}
+\title{straightenOperonSeq}
 \usage{
-reverse_operon(prot)
+straightenOperonSeq(prot)
 }
 \arguments{
 \item{prot}{}
 }
 \description{
-reverse_operon
+straightenOperonSeq
 }
diff --git a/man/to_titlecase.Rd b/man/to_titlecase.Rd
deleted file mode 100644
index 45139d3b..00000000
--- a/man/to_titlecase.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/pre-msa-tree.R
-\name{to_titlecase}
-\alias{to_titlecase}
-\alias{totitle,}
-\alias{to_title}
-\title{To Titlecase}
-\usage{
-to_titlecase(text, delimitter)
-}
-\arguments{
-\item{x}{Character vector.}
-
-\item{y}{Delimitter. Default is space (" ").}
-}
-\description{
-Translate string to Title Case w/ delimitter.
-Changing case to 'Title Case'
-}
-\seealso{
-chartr, toupper, and tolower.
-}
-\author{
-Andrie, Janani Ravi
-}
diff --git a/man/write.MsaAAMultipleAlignment.Rd b/man/writeMSA_AA2FA.Rd
similarity index 65%
rename from man/write.MsaAAMultipleAlignment.Rd
rename to man/writeMSA_AA2FA.Rd
index 17a05f50..a6798469 100644
--- a/man/write.MsaAAMultipleAlignment.Rd
+++ b/man/writeMSA_AA2FA.Rd
@@ -1,12 +1,12 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R
-\name{write.MsaAAMultipleAlignment}
-\alias{write.MsaAAMultipleAlignment}
-\title{Write MsaAAMultpleAlignment Objects as algined fasta sequence}
+\name{writeMSA_AA2FA}
+\alias{writeMSA_AA2FA}
+\title{writeMSA_AA2FA}
 \usage{
-write.MsaAAMultipleAlignment(alignment, outpath)
+writeMSA_AA2FA(alignment, outpath)
 
-write.MsaAAMultipleAlignment(alignment, outpath)
+writeMSA_AA2FA(alignment, outpath)
 }
 \arguments{
 \item{alignment}{MsaAAMultipleAlignment object to be written as a fasta}
@@ -17,7 +17,7 @@ write.MsaAAMultipleAlignment(alignment, outpath)
 MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
 and msaMuscle from the 'msa' package
 
-Write MsaAAMultpleAlignment Objects as algined fasta sequence
+Write MsaAAMultpleAlignment Objects as aligned fasta sequence
 MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
 and msaMuscle from the 'msa' package
 }