HAPAR – Haplotype Inference by Parsimony

HAPAR

:: DESCRIPTION

HAPAR (Haplotype Inference by Parsimony) is a program to infer haplotype from genotype data. It uses the parsimony principle, i.e. try to find the minimum number of haplotypes that can reconstruct the input genotypes.

::DEVELOPER

Lusheng Wang ,  Ying Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /UNIX

:: DOWNLOAD

 HAPAR

:: MORE INFORMATION

Citation

Lusheng Wang, Ying Xu,
Haplotype Inference by Parsimony,
Bioinformatics, 19(14), 2003.

PhySca – SCJ small parsimony problem for weighted Gene Adjacencies

PhySca

:: DESCRIPTION

PhySca samples solutions to the Single-Cut-and-Join (SCJ) small parsimony problem for weighted gene adjacencies.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PhySca

:: MORE INFORMATION

Citation

Luhmann N, Lafond M, Thevenin A, Ouangraoua A, Wittler R, Chauve C.
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1364-1373. doi: 10.1109/TCBB.2017.2661761. Epub 2017 Jan 31. PMID: 28166504.

TNT 202106 – Phylogenetic Analysis under Parsimony

TNT 202106

:: DESCRIPTION

TNT (Tree Analysis using New Technology) is a program for phylogenetic analysis under parsimony , as well as extensive tree handling and diagnosis capabilities.

::DEVELOPER

TNT team

:: SCREENSHOTS

TNT

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 TNT

:: MORE INFORMATION

Citation

Giribet G.
TNT: Tree Analysis Using New Technology.”.
Syst Biol. 2005;54:176-178.

RPOLY 1.2.1 – Inference of Haplotypes by Pure Parsimony

RPOLY 1.2.1

:: DESCRIPTION

RPoly is a software to infer haplotypes from genotype data using the pure parsimony criterion, i.e., find the minimum number of haplotypes which explain a given set of genotypes. Rpoly is an efficient tool which uses pseudo-Boolean optimization to solve haplotype inference by pure parsimony.

::DEVELOPER

Ana Sofia Graça

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 RPoly

:: MORE INFORMATION

Citation

A. Graça, J. P. Marques-Silva, I. Lynce and A. Oliveira,
Efficient Haplotype Inference with Pseudo-Boolean Optimization,
Algebraic Biology 2007, July 2007.

A. Graça, J. P. Marques-Silva, I. Lynce and A. Oliveira,
Efficient Haplotype Inference with Combined CP and OR Techniques (Short Paper),
CPAIOR 2008, May 2008.

DLCpar v1.1 – Reconciles Gene Trees to Species Trees through Maximum Parsimony

DLCpar v1.1

:: DESCRIPTION

DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).

::DEVELOPER

Yi-Chieh Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • NetworkX

:: DOWNLOAD

DLCpar

:: MORE INFORMATION

Citation

Genome Res, 24 (3), 475-86 Mar 2014
Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep Coalescence Using Labeled Coalescent Trees
Yi-Chieh Wu , Matthew D Rasmussen, Mukul S Bansal, Manolis Kellis

Softparsmap – Gene Tree Species Tree Reconicilation using Parsimony

Softparsmap

:: DESCRIPTION

Softparsmap is a java package that uses ’soft parsimony’ to root gene trees by mapping them on to a species tree.

::DEVELOPER

Liberles Research Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Softparsmap

:: MORE INFORMATION

Citation

J Mol Evol. 2006 Aug;63(2):240-50. Epub 2006 Jul 7.
Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.
Berglund-Sonnhammer AC1, Steffansson P, Betts MJ, Liberles DA.

PRAP 2.0b3 – Parsimony & Likelihood Ratchet Analysis with PAUP*

PRAP 2.0b3

:: DESCRIPTION

PRAP (Parsimony and likelihood ratchet analyses with PAUP*) allows the calculation of Bremer support (BS, Decay values; Bremer 1988) using the parsimony ratchet algorithm (Nixon, 1999). Alternatively, BS can also be computed without using the ratchet.In addition, simple Parsimony Ratchet searches can be performed with PRAP, also by superposing random addition cycles onto the published ratchet procedure (Nixon, 1999) to further decrease the slight risk that even the Ratchet gets stuck in a single series of cycles. Here, a series of ratchet iterations (commonly about 200 iterations) is repeatedly started from different starting trees, and shortest trees from all these iterations series are collected.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

PRAP

:: MORE INFORMATION

Citation

Müller K
The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support
BMC Evolutionary Biology 2005, 5:58

Parsimonator 1.02 – Fast open-source Parsimony program

Parsimonator 1.02

:: DESCRIPTION

Parsimonator is a no-frills light-weight implementation for building starting trees under parsimony for RAxML-Light

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Parsimonator

:: MORE INFORMATION

PaPaRa 2.5 – PArsimony-based Phylogeny-Aware Read alignment program

PaPaRa 2.5

:: DESCRIPTION

PaPaRa is a PArsimony-based Phylogeny-Aware Read alignment program

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • C Compier

:: DOWNLOAD

 PaPaRa

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Aug 9;13:196. doi: 10.1186/1471-2105-13-196.
Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.
Alachiotis N, Berger SA, Stamatakis A.

GRAPPA 2.0 – Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

GRAPPA 2.0

:: DESCRIPTION

GRAPPA is software for Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithm.

::DEVELOPER

Bernard Moret

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 GRAPPA 

:: MORE INFORMATION

Citation

Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M.,
A new implementation and detailed study of breakpoint analysis,”
Proc. 6th Pacific Symp. on Biocomputing (PSB 2001), Hawaii, World Scientific Pub. (2001), 583-594.