marekborowiec

#! /usr/bin/env python3

from amas import AMAS
from glob import glob

# glob all fasta files into a list
in_fs = glob('*.fasta')

# get a list of alignments in
meta_aln = AMAS.MetaAlignment(in_files=in_fs, data_type="dna",in_format="fasta", cores=1)

marekborowiec

library("ape")
library("data.table")

### SET WORKING DIRECTORY ###

setwd("/home/mlb/Dropbox/Misof_et_al_Science/Supplementary_Archive_2/aa_final_alignments/trees")

### READ IN TREE FILES ###

tree_files <- dir(pattern="*bipartitions.EOG*")

marekborowiec

#! /usr/bin/env python3

with open('miltons-numbers') as f:
	records = f.readlines()
	for record in records:
		if '.' not in record:
			first, sep, tail = record.partition('-')
			last, sep2, tail2 = tail.partition(' ')
			digits = len(last)
			to_prefix = first[:len(first) - digits]