seq (Seq)

seqIO

• convert fastq into fasta

  bio seq --input ./data/seq.fq --output ./data/seq.fa
  

• format fasta with max number of characters per line

  bio seq --input ./data/seq.fq --output ./data/seq_formated.fa --fasta-line-length 20
  

• subset records with list of names

  bio seq --input ./data/seq.fq --output ./data/seq_subset.fa --filter-names ./data/name.list
  

• subsamples N records

  bio seq --input ./data/seq.fq --output ./data/seq_sampled.fa --sample 2 --sample-seed 123
  

• trim DNA records

  bio seq --input ./data/seq.fq --output ./data/seq_sample.fa --trim-start 6 --trim-end 3
  

alignIO

phylo (Phylo)

treeIO

popgen