fishlifeqc

Features:

• quality control for exon alignments

Software requierements:

• pip
• python-dev

Installation

Using pip:

pip install fishlifeqc

Using git and pip (Optional):

git clone https://github.com/ulises-rosas/fishlifeqc.git 
cd fishlifeqc
python3 -m pip install .

Usage

Main command:

fishlifeqc -h

usage: fishlifeqc [-h] {mdata,rblast,bold,tlike,bl,para,srh} ...

                                 Quality Control Steps
                                      

positional arguments:
  {mdata,rblast,bold,tlike,bl,para,srh}
    mdata               Trim sequences in function of gap ocurrences
    rblast              Reciprocal blastn comparing taxonomical groups
    bold                Match sequences against the BOLD database
    tlike               Find T-like clades in trees
    bl                  Branch length ratios and correlations
    para                Test paraphyly with AU tests
    srh                 Test stationarity, reversibility and homogeneity

optional arguments:
  -h, --help            show this help message and exit

Utilities command:

qcutil -h

usage: qcutil [-h] {qstats,fstats,itt,rf,delete,knockdown} ...

                                 Utilities from fishlifeqc
                                      

positional arguments:
  {qstats,fstats,itt,rf,delete,knockdown}
    qstats              quick summary of alignment information
    fstats              full summary of both alignment and tree information
    itt                 Incongruence through time
    rf                  Robinson-Foulds distances
    delete              Delete specific sequences from files
    knockdown           Replace specific codon positions with 'N's

optional arguments:
  -h, --help            show this help message and exit

A description of summary statistics currently available for qcutil can be found here.

Yet unintegrated scripts into qcutil:

• merge.py : join two set of exons by using a map file
• concatenate.py : concatenate exons
• codon_partition.py : generate a condon partition file
• cons_trees.py : for each exon, constrain a reference tree by exon taxa
• collapse.py : collapse edges in function of support values