fasta

fai2bed.py

creates a bed file from a fai file. samtools faidx FOO.fa python fai2bed.py FOO.fa.fai # > pos.bed bedtools getfasta -fi FOO.fa -bed pos.bed -tab -bedOut > FOO.bed

fasta2phy.py

Convert fasta alignemnts to relaxed phylip ones in constant memory. Written by Lucas Sinclair; James B. Pease fasta2phy.py IN.fasta OUT.phylip

fasta2raxml.py

Written by Jon Palmer (2016) [email protected] Script runs Mafft -> trimAl -> RAxML. takes multi-fasta as input

fastarenamefromfilename.py

renames the header in the fasta file from the file name

firstFasta.py

prints the first entry from a multifasta

gff2fastaAln.py

Using a gff file it parses out individual alignments of exons and non-coding sequences python gff2fastaAln.py --gff FOO.gff --aln FOO.aln.fa [--exons] [--distance int] [--length int] [--chromlen int]

reverse_fasta.py

reverses sections of a fasta file given by coordinates. Useful for correcting small artifact inversions. Some hard-coding.

sfsFromFasta.py

returns the site frequency spectrum from a fasta file sfsFromFasta.py --fasta FOO.fa --ancestral FOO.anc.fa