seqSieve 0.9.3

seqSieve
===========

Installation:

pip install seqSieve

This should also install numpy and matplotlib automatically if necessary.
If you have trouble installing dependencies via pip, try installing
them with your distribution's package manager.

On debian do:

apt-get install python-matplotlib python-numpy

It is also possible to run seqSieve without installation

python seqSieve/seqSieve



**seqSieve** will try to remove sequences that cause misalignments from a multiple sequence alignment(MSA).
It reads a given MSA in multi-fasta format and removes sequences with the highest penalty scores,
then builds the next MSA without those sequences. This process is repeated until a user-specified
cut-off is reached or less than three sequences are left to be aligned.

In the default mode "Sites", sequences are penalized for both gaps and insertions by an amount proportional to the percentage of ungapped and gapped sequences, respectively.
The modes "Gaps", "uGaps","Insertions", "uInsertions","uInsertionsGaps" always assign a penalty of 1 for the named variation. "u" stands for unique, i.e. uGaps only penalizes unique gaps.
With mode "custom" the user sets the penalties for each variation.

Usage:

######################################
# seqSieve
######################################
usage:
seqSieve -f multifasta alignment
options:
-f, --fasta=FILE multifasta alignment (eg. "align.fas")
OR
-F, --fasta_dir=DIR directory with multifasta files (needs -s SUFFIX)
-s, --suffix=SUFFIX will try to work with files that end with SUFFIX (eg ".fas")

-a, --msa_tool=STR supported: "mafft", prank, prankf (= prank +F) [default:"mafft"]
-i, --max_iterations=NUM force stop after NUM iterations
-n, --num_threads=NUM max number of threads to be executed in parallel [default: 1]
-m, --mode=MODE set strategy to remove outlier sequences [default: "Sites"]
available modes (not case sensitive):
"Sites", "Gaps", "uGaps","Insertions",
"uInsertions","uInsertionsGaps", "custom"
-q, --no-realign don't realign with each iteration (not recommended)
-l, --log write logfile
-h, --help prints this

only for mode "custom":
-g, --gap_penalty=NUM set gap penalty [default: 1.0]
-G, --unique_gap_penalty=NUM set unique gap penalty [default: 10.0]
-j, --insertion_penalty=NUM set insertion penalty [default:1.0]
-J, --unique_insertion_penalty=NUM set insertion penalty [default:1.0]
-M, --mismatch_penalty=NUM set mismatch penalty [default:1.0]
-r, --match_reward=NUM set match reward [default: -10.0]


Currently supported multiple sequence aligners:

- mafft (Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780)
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. http://mafft.cbrc.jp/alignment/software/)
- prank (Loytynoja, Goldman 2005 (PNAS 102:10557-10562)
An algorithm for progressive multiple alignment of sequences with insertions. http://www.ebi.ac.uk/goldman-srv/prank/prank/

Requirements
============
* matplotlib
* numpy

External Programs
-----------------
* mafft and/or
* prank