Update versioning to v0.4a2

justincbagley · Apr 17, 2020 · e7e442a · e7e442a
1 parent 0f98147
commit e7e442a
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Showing 60 changed files with 80 additions and 75 deletions.
diff --git a/bin/AnouraNEXUSPrepper b/bin/AnouraNEXUSPrepper
@@ -281,7 +281,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
  Sierra (10.13+) and many earlier macOS or OSX versions.
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/BEASTPostProc b/bin/BEASTPostProc
@@ -452,7 +452,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f BEASTPostProc -h       Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/BEASTReset b/bin/BEASTReset
@@ -294,11 +294,11 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f BEASTReset -h                                Print help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  Created by Justin Bagley on Thu, 24 Aug 2017 11:30:42 -0400.

diff --git a/bin/BEASTRunner b/bin/BEASTRunner
@@ -418,7 +418,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f BEASTRunner -n 10 -w 24:00:00 -m 2048M     Change memory (RAM) allocation to 2GB
 	
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -496,7 +496,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f BEASTRunner -n 10 -w 24:00:00 -m 2048M     Change memory (RAM) allocation to 2GB
 	
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/BEAST_PSPrepper b/bin/BEAST_PSPrepper
@@ -355,7 +355,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f BEAST_PSPrepper -h       Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/BEAST_logThinner b/bin/BEAST_logThinner
@@ -236,7 +236,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f BEAST_logThinner -h       Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/ExaBayesPostProc b/bin/ExaBayesPostProc
@@ -428,7 +428,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f ExaBayesPostProc -h                   Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/FASTA2PHYLIP b/bin/FASTA2PHYLIP
@@ -1009,7 +1009,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
                                                               keep FASTAs, and echo run output to screen
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -1092,7 +1092,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
                                                               keep FASTAs, and echo run output to screen
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/FASTA2VCF b/bin/FASTA2VCF
@@ -420,7 +420,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f FASTA2VCF -h                                                         Print this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/FASTAsummary b/bin/FASTAsummary
@@ -444,7 +444,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f FASTAsummary -m 1                Summarize multiple FASTA files
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  Created by Justin Bagley on Fri, Apr 3 00:03:39 EDT 2020.

diff --git a/bin/MAGNET-1.1.1/MAGNET b/bin/MAGNET-1.1.1/MAGNET
@@ -1036,7 +1036,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f MAGNET -h                                  Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -1157,7 +1157,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f MAGNET -h                                  Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/MLEResultsProc b/bin/MLEResultsProc
@@ -348,7 +348,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f MLEResultsProc -h      Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  Created by Justin Bagley on Fri, 29 Jul 2016 11:21:37 -0300.

diff --git a/bin/Mega2PHYLIP b/bin/Mega2PHYLIP
@@ -380,7 +380,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f Mega2PHYLIP -h                       Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/MrBayesPostProc b/bin/MrBayesPostProc
@@ -433,7 +433,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f MrBayesPostProc -h
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/NEXUS2MultiPHYLIP b/bin/NEXUS2MultiPHYLIP
@@ -559,7 +559,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f NEXUS2MultiPHYLIP -h                        Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/NEXUS2PHYLIP b/bin/NEXUS2PHYLIP
@@ -451,7 +451,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
                                                           file (if present)
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -513,7 +513,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
                                                           file (if present)
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/PFSubsetSum b/bin/PFSubsetSum
@@ -324,7 +324,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PFSubsetSum -h      Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
@@ -354,7 +354,7 @@ if [[ "$1" == "-h" ]] || [[ "$1" == "--help" ]]; then
 fi
 
 if [[ "$1" == "-c" ]] || [[ "$1" == "-citation" ]] || [[ "$1" == "--citation" ]]; then
-	echo " Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+	echo " Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 "
 	exit

diff --git a/bin/PHYLIP2FASTA b/bin/PHYLIP2FASTA
@@ -367,7 +367,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
                                                        print stdout to screen
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/PHYLIP2Mega b/bin/PHYLIP2Mega
@@ -378,7 +378,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PHYLIP2Mega -m1 -k 1                  Convert multiple PHYLIP files to Mega format, keeping original files
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/PHYLIP2NEXUS b/bin/PHYLIP2NEXUS
@@ -390,7 +390,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PHYLIP2NEXUS -m 1 
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/PHYLIP2PFSubsets b/bin/PHYLIP2PFSubsets
@@ -456,7 +456,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PHYLIP2PFSubsets -h      Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  Created by Justin Bagley on Tue, Mar 5 09:53:04 CST 2019.

diff --git a/bin/PHYLIPcleaner b/bin/PHYLIPcleaner
@@ -406,7 +406,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PHYLIPcleaner -h                        Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/PHYLIPsubsampler b/bin/PHYLIPsubsampler
@@ -347,7 +347,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PHYLIPsubsampler -h                  Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/PHYLIPsummary b/bin/PHYLIPsummary
@@ -272,7 +272,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PHYLIPsummary -h                    Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/PhyloMapperNullProc b/bin/PhyloMapperNullProc
@@ -217,7 +217,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f PhyloMapperNullProc -h      Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/RAxMLRunChecker b/bin/RAxMLRunChecker
@@ -262,7 +262,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
 
  ${bold}OVERVIEW${reset}
  THIS SCRIPT was designed to run in a current working directory where the MAGNET pipeline
- in PIrANHA v0.4a (Bagley 2020) is being run, or has completed a run, to estimate maximum-
+ in PIrANHA v0.4a2 (Bagley 2020) is being run, or has completed a run, to estimate maximum-
  likelihood (ML) gene trees in RAxML v8+ (Stamatakis 2014) for a set of loci from DNA 
  sequence data. Given such a workspace, this script counts the number of loci or data 
  partitions (each assigned a separate RAxML run in MAGNET) with completed RAxML runs and 
@@ -280,11 +280,11 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f RAxMLRunChecker -h      Print this help text
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
  Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of 
 	large phylogenies. Bioinformatics, 30, 1312-1313.

diff --git a/bin/RAxMLRunner b/bin/RAxMLRunner
@@ -323,7 +323,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f RAxMLRunner -h      Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/README.md b/bin/README.md
@@ -58,6 +58,7 @@ The full file tree for this directory is as follows:
    ├── NEXUS2PHYLIP
    ├── nQuireRunner
    ├── PFSubsetSum
+   ├── phaseAlleles
    ├── PHYLIP2FASTA
    ├── phylip2fasta.pl
    ├── PHYLIP2Mega
@@ -80,6 +81,7 @@ The full file tree for this directory is as follows:
    ├── splitFile
    ├── splitPHYLIP
    ├── taxonCompFilter
+   ├── test
    ├── treeThinner
    ├── vcfSubsampler
    └── virtualenv.txt

diff --git a/bin/RYcoder b/bin/RYcoder
@@ -423,7 +423,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f RYcoder -h                         Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/RogueNaRokRunner b/bin/RogueNaRokRunner
@@ -309,7 +309,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f RogueNaRokRunner -h                     Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/SNAPPRunner b/bin/SNAPPRunner
@@ -560,7 +560,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f SNAPPRunner -h                              Show this help text and exit
 	
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/PIrANHA>.
 
  ${bold}REFERENCES${reset}
@@ -645,7 +645,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f SNAPPRunner -h                              Show this help text and exit
 	
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/SpeciesIdentifier b/bin/SpeciesIdentifier
@@ -304,7 +304,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f SpeciesIdentifier -h      Show this help text and exit
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/calcAlignmentPIS b/bin/calcAlignmentPIS
@@ -459,7 +459,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
                                                    R input and output files generated during run
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}

diff --git a/bin/completeConcatSeqs b/bin/completeConcatSeqs
@@ -454,7 +454,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
 		piranha -f completeConcatSeqs -t taxon_name_spaces12.txt -v 1
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  Created by Justin Bagley on Tue, Mar 12 19:11:08 CDT 2019.

diff --git a/bin/completeSeqs b/bin/completeSeqs
@@ -372,7 +372,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
 		piranha -f completeSeqs -t taxon_name_spaces12.txt -v 1
 
  ${bold}CITATION${reset}
- Bagley, J.C. 2020. PIrANHA v0.4a. GitHub repository, Available at:
+ Bagley, J.C. 2020. PIrANHA v0.4a2. GitHub repository, Available at:
 	<https://github.com/justincbagley/piranha>.
 
  ${bold}REFERENCES${reset}