ConstraintChecker – Test Satisfiability/Consistency with Species Tree

ConstraintChecker

:: DESCRIPTION

ConstraintChecker is a python script that tests satisfiability/consistency with a species tree of a set of orthologies/paralogies/undecided.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 ConstraintChecker

:: MORE INFORMATION

Citation

Manuel Lafond and Nadia El-Mabrouk
“Orthology and Paralogy Constraints: Satisfiability and Consistency”
RECOMB-CG 2014 paper (accepted)

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