Features:
- quality control for exon alignments
Software requierements:
- pip
- python-dev
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 .
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 fileconcatenate.py
: concatenate exonscodon_partition.py
: generate a condon partition filecons_trees.py
: for each exon, constrain a reference tree by exon taxacollapse.py
: collapse edges in function of support values