diff --git a/bin/AnouraNEXUSPrepper b/bin/AnouraNEXUSPrepper
index b644e17d..8e7bdefd 100755
--- 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
index 331a8efe..638d000a 100755
--- 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
index f2259f42..a2111081 100755
--- 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
index 5ce85449..cb1b60e7 100755
--- 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
index d0a0ff22..40476756 100755
--- 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
index 1c3cfbcd..455e0b31 100755
--- 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
index 0ddea48b..31b8e2a0 100755
--- 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
index cafb0a5e..932d96db 100755
--- 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
index 35831a66..7fa3868c 100755
--- 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
index e2a67e76..bcb62b75 100755
--- 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
index 282902a5..1cbc71e3 100644
--- 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
index 2f4ba6fb..da64e087 100755
--- 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
index fbea3f84..76343579 100755
--- 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
index 5cc1c53b..1f4fb845 100755
--- 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
index 84da72bc..73528845 100755
--- 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
index 70031231..d33d3d41 100755
--- 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
index 561f57b7..5b96b4d1 100755
--- 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
index ee830198..d8ce1b39 100755
--- 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
index 97136246..4d9e229c 100755
--- 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
index be99d39c..3932625b 100755
--- 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
index f6ba1365..5df43924 100755
--- 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
index 89e30a3a..2878bd17 100755
--- 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
index 55cafe92..34b3bb58 100755
--- 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
index 446ff759..bd7855ac 100755
--- 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
index 3a0ff35c..9a9b4ed8 100755
--- 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
index 7914bd5b..eba0f626 100755
--- 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
index e997e342..e0aee388 100755
--- 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
index 1543d541..a05cc524 100755
--- 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
index cc763914..41847432 100755
--- 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
index 02907c20..993af619 100755
--- 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
index 354eb456..08451802 100755
--- 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
index 3b9ba98d..077860c0 100755
--- 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
index cfce48e3..dab057bb 100755
--- 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
index f4d5e353..5f044b9a 100755
--- 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
index ea382390..0d63448d 100755
--- 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}
diff --git a/bin/concatSeqsPartitions b/bin/concatSeqsPartitions
index 183f33c7..b576c228 100755
--- a/bin/concatSeqsPartitions
+++ b/bin/concatSeqsPartitions
@@ -369,7 +369,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
 		piranha -f concatSeqsPartitions -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}
diff --git a/bin/concatenateSeqs b/bin/concatenateSeqs
index ba346c3c..4c2d49cd 100755
--- a/bin/concatenateSeqs
+++ b/bin/concatenateSeqs
@@ -345,7 +345,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
 		piranha -f concatenateSeqs -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}
diff --git a/bin/dadiPostProc b/bin/dadiPostProc
index a74ddba9..d14b0a4c 100755
--- a/bin/dadiPostProc
+++ b/bin/dadiPostProc
@@ -411,7 +411,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
                                                  ranges starting from values other than 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}
@@ -463,7 +463,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
                                                  ranges starting from values other than 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/dadiRunner b/bin/dadiRunner
index e9df09bd..cd13f4a8 100755
--- a/bin/dadiRunner
+++ b/bin/dadiRunner
@@ -417,7 +417,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f dadiRunner -i <SNPInput> -n 20 -w 24:00:00      Changing run walltime.
 
  ${bold}CITATION${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}
@@ -493,7 +493,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f dadiRunner -i <SNPInput> -n 20 -w 24:00:00      Changing run walltime.
 	
  ${bold}CITATION${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/dadiUncertainty b/bin/dadiUncertainty
index 8afe5cde..ca03d079 100755
--- a/bin/dadiUncertainty
+++ b/bin/dadiUncertainty
@@ -972,7 +972,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f dadiUncertainty -a assignments.txt -i \'LP\',\'core\',\'periphery\' -p 98,46,156 -n 250 -m 2 -s M4.py -e 0.72828532,0.29458734,0.96806661,5.30191219,6.90827885,4.35076242,8.80921022,0.0349316,0.00881585 55Pops.recode.6330IDs.vcf
  
  ${bold}CITATION${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/dropRandomHap b/bin/dropRandomHap
index fb5330ba..0257c118 100755
--- a/bin/dropRandomHap
+++ b/bin/dropRandomHap
@@ -388,7 +388,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
 		piranha -f dropRandomHap -t <numTips>_taxon_names.txt
 
  ${bold}CITATION${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/dropTaxa b/bin/dropTaxa
index 0a6e2633..c327f4bb 100755
--- a/bin/dropTaxa
+++ b/bin/dropTaxa
@@ -585,7 +585,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f dropTaxa -m 1 -f phylip -t <taxonList> -k 1               Drop taxa from multiple PHYLIP files, keep 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/fastSTRUCTURE b/bin/fastSTRUCTURE
index eb52bbb2..09d06f56 100755
--- a/bin/fastSTRUCTURE
+++ b/bin/fastSTRUCTURE
@@ -224,7 +224,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f fastSTRUCTURE -p <fsPath> -i <fsInput> -l <lowerK> -u <upperK> -o <fsOutput>
 
  ${bold}CITATION${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/getBootTrees b/bin/getBootTrees
index 4f27fd57..4da81580 100755
--- a/bin/getBootTrees
+++ b/bin/getBootTrees
@@ -216,7 +216,7 @@ 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) has been run to estimate maximum-likelihood (ML) gene trees 
+ in PIrANHA v0.4a2 (Bagley 2020) has been 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 organizes the bootstrap trees resulting from all RAxML runs, in
  subfolders of the current directory. The getBootTrees function is already run during the
@@ -237,11 +237,11 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f getBootTrees -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}
- 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/getTaxonNames b/bin/getTaxonNames
index d5883b37..8b0b8850 100755
--- a/bin/getTaxonNames
+++ b/bin/getTaxonNames
@@ -264,7 +264,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f getTaxonNames -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 Wed, Mar 13 17:17:41 CDT 2019.
diff --git a/bin/makePartitions b/bin/makePartitions
index f050a35b..6a301f90 100755
--- a/bin/makePartitions
+++ b/bin/makePartitions
@@ -304,7 +304,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f makePartitions -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/nQuireRunner b/bin/nQuireRunner
index 69782a8f..4a8a5e71 100755
--- a/bin/nQuireRunner
+++ b/bin/nQuireRunner
@@ -480,7 +480,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f nQuireRunner -m 1               Multi-BAM run on all .bam files in working directory
 
  ${bold}CITATION${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}
@@ -533,7 +533,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f nQuireRunner -m 1               Multi-BAM run on all .bam files in working directory
 
  ${bold}CITATION${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/phaseAlleles b/bin/phaseAlleles
index 1400952e..5a3c9185 100644
--- a/bin/phaseAlleles
+++ b/bin/phaseAlleles
@@ -498,7 +498,7 @@ Usage: piranha -f $(basename "$0") [Options]...
     piranha -f phaseAlleles -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/phyNcharSumm b/bin/phyNcharSumm
index da1d0ee6..2087e537 100755
--- a/bin/phyNcharSumm
+++ b/bin/phyNcharSumm
@@ -194,7 +194,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f phyNcharSumm
 
  ${bold}CITATION${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 November 9, 2016.
@@ -210,7 +210,7 @@ if [[ "$1" == "-V" ]] || [[ "$1" == "--version" ]]; then
 fi
 
 if [[ "$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/pyRAD2PartitionFinder b/bin/pyRAD2PartitionFinder
index bacf455c..3f8d09ad 100755
--- a/bin/pyRAD2PartitionFinder
+++ b/bin/pyRAD2PartitionFinder
@@ -402,7 +402,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f pyRAD2PartitionFinder -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/pyRADLocusVarSites b/bin/pyRADLocusVarSites
index bce0abb0..1084dacf 100755
--- a/bin/pyRADLocusVarSites
+++ b/bin/pyRADLocusVarSites
@@ -261,7 +261,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f pyRADLocusVarSites -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/renameForStarBeast2 b/bin/renameForStarBeast2
index 18920a57..0da83b47 100755
--- a/bin/renameForStarBeast2
+++ b/bin/renameForStarBeast2
@@ -274,7 +274,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f renameForStarBEAST2 -f fasta -a <assignmentFile>
 
  ${bold}CITATION${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/renameTaxa b/bin/renameTaxa
index cef27e62..468be9ff 100755
--- a/bin/renameTaxa
+++ b/bin/renameTaxa
@@ -388,11 +388,11 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f renameTaxa -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}
- 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 Wed, Apr 10 08:43:01 CDT 2019.
diff --git a/bin/splitFASTA b/bin/splitFASTA
index 5129e4bb..9b08b156 100644
--- a/bin/splitFASTA
+++ b/bin/splitFASTA
@@ -405,7 +405,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f FASTA2PHYLIP -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 Wed, Apr 1 12:05:32 CDT 2020.
@@ -452,7 +452,7 @@ VERBOSE_USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f FASTA2PHYLIP -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 Wed, Apr 1 12:05:32 CDT 2020.
diff --git a/bin/splitFile b/bin/splitFile
index 17e30a57..5a195488 100755
--- a/bin/splitFile
+++ b/bin/splitFile
@@ -291,7 +291,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f splitFile -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 Sat, April 4 10:54:22 CDT 2020.
diff --git a/bin/splitPHYLIP b/bin/splitPHYLIP
index 15d03729..12301a0d 100755
--- a/bin/splitPHYLIP
+++ b/bin/splitPHYLIP
@@ -325,7 +325,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f splitPHYLIP -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/taxonCompFilter b/bin/taxonCompFilter
index beefc9bb..77375c7e 100755
--- a/bin/taxonCompFilter
+++ b/bin/taxonCompFilter
@@ -317,7 +317,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f taxonCompFilter -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/treeThinner b/bin/treeThinner
index 17d4d923..c9418950 100755
--- a/bin/treeThinner
+++ b/bin/treeThinner
@@ -212,7 +212,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f treeThinner
 
  ${bold}CITATION${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/vcfSubsampler b/bin/vcfSubsampler
index 70492c1a..f67e4a01 100755
--- a/bin/vcfSubsampler
+++ b/bin/vcfSubsampler
@@ -213,7 +213,7 @@ USAGE="Usage: $(basename "$0") [OPTION]...
     piranha -f vcfSubsampler -i <inputVCFFile> -s <snpsFile>      
 
  ${bold}CITATION${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 Thu, Sep 28 09:31:25 2017 -0400.
diff --git a/piranha b/piranha
index 32294b7d..ea5c0c62 100755
--- a/piranha
+++ b/piranha
@@ -271,6 +271,9 @@ nQuireRunner           Function that automates running nQuire software (Weiß et
                        starting from BAM file(s) for the sample(s)
 PFSubsetSum            Calculates summary statistics for DNA subsets within the optimum partitioning scheme 
                        identified for the data by PartitionFinder v1 or v2 (Lanfear et al. 2012, 2014).
+phaseAlleles           Automates phasing alleles of HTS data from targeted sequence capture experiments (or similar), 
+                       including optionally transferring indel gaps from reference to the final phased FASTAs of 
+                       consensus sequences, by masking
 PHYLIP2FASTA           Automates converting each of one or multiple PHYLIP DNA sequence alignments into FASTA 
                        format.
 phylip2fasta.pl        Nayoki Takebayashi utility Perl script for converting from PHYLIP to FASTA format.