phylo_scripts

This is an unsorted collection of small(mostly) and handy scripts I use for my daily work.

phylip2fasta.sh and nexus2fasta.sh: For quickly converting a PHYLIP or nexus formatted supermatrix to a simple FASTA file. PHYLIP file does not have any taxon id restrictions other than there needs to be at least one space after each taxon id.
concat-aln: concatenate a set of fasta formatted alignments to a relaxed PHYLIP formatted supermatrix using Biopython. Also writes a nexus file with partition information.
translate_stdin.py: Translate fasta formatted alignments (or codon sequences) passed in to standard input using Biopython.
clearEmptyFasta.awk: Clear fasta entries with empty sequences.
unwrapFasta.awk: Unwrap a fasta formatted file so that the sequence for each entry can only span a single line.
ncbi_download.sh: Find the latest versions of the list of genome accessions and download all genomes using ncbi command-line tools

Name		Name	Last commit message	Last commit date
Latest commit History 31 Commits
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
cleanAllGaps		cleanAllGaps
clearEmptyFasta.awk		clearEmptyFasta.awk
concat-aln		concat-aln
find_buscos.py		find_buscos.py
get_aln_len.awk		get_aln_len.awk
ignore3rdCodonPos.awk		ignore3rdCodonPos.awk
iqtree_to_raxml_models.awk		iqtree_to_raxml_models.awk
keep_taxa.awk		keep_taxa.awk
ncbi_download.sh		ncbi_download.sh
nexus2fasta.sh		nexus2fasta.sh
partitionbyCodon.awk		partitionbyCodon.awk
phylip2fasta.sh		phylip2fasta.sh
printEmptyFastaHeaders.awk		printEmptyFastaHeaders.awk
remove_taxa.awk		remove_taxa.awk
translate_stdin.py		translate_stdin.py
unalignFasta.awk		unalignFasta.awk
unwrapFasta.awk		unwrapFasta.awk

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