All should be considered beta versions, and they my require a bit of tweaking to work.
Some take command line arguments, and some you have to edit the script itself.
You can e-mail me (below) with questions, problems, or suggestions. For additional scripts, check our public code repo on bitbucket...
[encodename.pl] convert fasta file with long names to phylip with short names. useful for phyml and raxml. also can concatenate sequences or convert some file formats
[decodename.pl] convert short names generated by encodename.pl back into long names, for example in a tree file. can also edit the lookup table to clean up or annotations to tree names
[protcalc.pl] from a fasta file of amino acid sequences, print out a list of calculated values including molecular weight, charge, and percent composition. also search proteins for short motifs [translateone.py] read a fasta file, do 6-frame translation, print best protein seqs as fasta [mybio.py] mini library required for use with translatedna, seqlite and filterseqs [genbanknames.py] retrieve genbank records from accession numbers [blastplustable.py] perform blast searches on a fasta file, save abbreviated result table (requires biopython and local blast+ installation) [lucidconvert.py] Convert Lucid Builder CSV exported files to a NEXUS formatted table [seqlite_nohtml.py] from a sequence alignment, return only the variable sites and sequences. (requires mybio.py, above) [sizeonly.py] from a fasta file, return only the size of each sequence, for making a histogram, etc [gapmap.py] given an aligned amino acid file and a corresponding unaligned DNA file, insert gaps into the DNA file to create an alignment [smartcat.sh] join together multiple files as one, using *.fta formulation [findseqname.py] sort through a fasta file, keeping or rejecting sequences with names that contain a certain string. requires mybio.py, above [findmotif.py] sort through a fasta file, keeping or rejecting sequences which contain a certain subsequence. search can be specified as regexp: "ATG$". requires mybio.py, above
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