profileNJ 2016 – Genome Evolution-aware Gene Trees Correction

profileNJ 2016

:: DESCRIPTION

Given a non-binary gene tree, a species tree and an optional gene distance matrix, profileNJ outputs a binarization of the gene tree that minimizes the duplication+loss score.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

profileNJ

:: MORE INFORMATION

Citation

Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Guéguen L, El-Mabrouk N, Tannier E.
Efficient Gene Tree Correction Guided by Genome Evolution.
PLoS One. 2016 Aug 11;11(8):e0159559. doi: 10.1371/journal.pone.0159559. PMID: 27513924; PMCID: PMC4981423.

PCMA – Profile Consistency Multiple sequence Alignment

PCMA

:: DESCRIPTION

PCMA constructs a multiple sequence alignment given a set of protein sequences.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

PCMA

:: MORE INFORMATION

Citation:

J.Pei, R.I.Sadreyev, and N.V.Grishin (2003)
“PCMA: Fast and Accurate Multiple Sequence Alignment Based on Profile Consistency“.
Bioinformatics 19(3): 427-428.

CBA 200504 – Consistency Based Alignment

CBA 200504

:: DESCRIPTION

CBA (Consistency Based Alignment) builds multiple structure alignments from pairwise superpositions using consistency as a driving force.The software harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments.

::DEVELOPER

The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Complier

:: DOWNLOAD

CBA

:: MORE INFORMATION

Citation:

Jessica Ebert and Douglas Brutlag*
Development and validation of a consistency based multiple structure alignment algorithm
Bioinformatics (2006) 22 (9): 1080-1087