iBPP v2.1.3 – Bayesian Species Delimitation Integrating Genes and Traits data

iBPP v2.1.3

:: DESCRIPTION

iBPP is a program of integration of genes and traits for Bayesian Phylogenetics and Phylogeography.

::DEVELOPER

Solis-Lemus lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

iBPP

:: MORE INFORMATION

Citation

Solís-Lemus C, Knowles LL, Ané C.
Bayesian species delimitation combining multiple genes and traits in a unified framework.
Evolution. 2015 Feb;69(2):492-507. doi: 10.1111/evo.12582. Epub 2015 Jan 16. PMID: 25495061.

CatchAll 4.0 – Estimating the Number of Species

CatchAll 4.0

:: DESCRIPTION

CatchAll is a new, platform-independent, user-friendly, computationally optimized software package which calculates a powerful and flexible suite of parametric models (based on current statistical research) in addition to all existing nonparametric procedures.

::DEVELOPER

The Comai Lab

:: SCREENSHOTS

CatchAll

:: REQUIREMENTS

  • Linux / Windows
  • excel

:: DOWNLOAD

  CatchAll

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2011:121-30.
Estimating the number of species with CatchAll.
Bunge J.

ACES v.1.2 – Analysis of Conservation with an Extensive list of Species

ACES v.1.2

:: DESCRIPTION

ACES is a workflow to query small sequences in a large set of genomes. It provides several outputs including BLAST results, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file.

::DEVELOPER

TNTurnerLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Docker
:: DOWNLOAD

ACES

:: MORE INFORMATION

Citation

Padhi EM, Ng JK, Mehinovic E, Sams EI, Turner TN.
ACES: Analysis of Conservation with an Extensive list of Species.
Bioinformatics. 2021 Oct 2;37(21):3920–2. doi: 10.1093/bioinformatics/btab684. Epub ahead of print. PMID: 34601580; PMCID: PMC8570785.

sgp2 1.1 – Predict Genes by comparing Anonymous Genomic Sequences from two different Species

sgp2 1.1

:: DESCRIPTION

sgp2 is a program to predict genes by comparing anonymous genomic sequences from two different species. It combines tblastx, a sequence similarity search program, with geneid, an “ab initio” gene prediction program. In “assymetric” mode, genes are predicted in one sequence from one species (the target sequence), using a set of sequences (maybe only one) from the other species (the reference set). Essentially, geneid is used to predict all potential exons along the target sequence. Scores of exons are computed as log-likelihood ratios, function of the splice sites defining the exon, the coding bias in composition of the exon sequence as measured by a Markov Model of order five, and of the optimal alignment at the amino acid level between the target exon sequence and the counterpart homologous sequence in the reference set. From the set of predicted exons, the gene structure is assembled (eventually multiple genes in both strands) maximizing the sum of the scores of the assembled exons.

::DEVELOPER

RODERIC GUIGO LAB

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 sgp2

:: MORE INFORMATION

Citation

G. Parra, P. Agarwal, J.F. Abril, T. Wiehe, J.W. Fickett and R. Guigó.
Comparative gene prediction in human and mouse.”
Genome Research 13(1):108-117 (2003)

Saguaro 0.1 – Detect Signatures of Selection within Populations, Strains, or Species

Saguaro 0.1

:: DESCRIPTION

Saguaro (Genome-Wide) , SaguaroGW,is a program to detect signatures of selection within populations, strains, or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in the genome.

::DEVELOPER

the Science for Life Laboratory, Uppsala University, and the Broad Institute of MIT and Harvard.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Saguaro

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 May 24;14:347. doi: 10.1186/1471-2164-14-347.
Unsupervised genome-wide recognition of local relationship patterns.
Zamani N1, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG.

ecceTERA 1.2.4 – Gene Tree Species Tree Reconciliation

ecceTERA 1.2.4

:: DESCRIPTION

Given a (dated) species tree S, a set of gene trees G, and a set of costs for gene events (duplications, transfers and losses), ecceTERA computes the score of a most parsimonious reconciliation (MPR).

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ecceTERA

:: MORE INFORMATION

Citation

Jacox E, Chauve C, Szöllősi GJ, Ponty Y, Scornavacca C.
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.
Bioinformatics. 2016 Jul 1;32(13):2056-8. doi: 10.1093/bioinformatics/btw105. Epub 2016 Feb 26. PMID: 27153713.

OrthoRBH 1.1 – Rapidly Identify Orthologous cDNA Sequences in related Species

OrthoRBH 1.1

:: DESCRIPTION

OrthoRBH is a tool/pipeline designed to identify families of protein coding transcripts/genes in related species using a reciprocal blast method.

::DEVELOPER

OrthoRBH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OrthoRBH

:: MORE INFORMATION

Citation:

Bioinformation. 2013;9(5):267-9. doi: 10.6026/97320630009267. Epub 2013 Mar 2.
OrthoRBH: A streamlined pipeline for mining large gene family sequences in related species.
Ziemann M1, Kamboj A, Bhave M.

MUGBAS 20150313 – Species free Gene-based Programme Suite for Post-GWAS Analysis

MUGBAS 20150313

:: DESCRIPTION

MUGBAS (MUlti species Gene-Based Association Suite) is a open source pipeline for obtaining gene based results from a given GWA study.

::DEVELOPER

MUGBAS team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX
  • R
  • Perl
  • Python

:: DOWNLOAD

 MUGBAS

:: MORE INFORMATION

Citation:

MUGBAS: a species free gene-based programme suite for post-GWAS analysis.
Capomaccio S, Milanesi M, Bomba L, Vajana E, Ajmone Marsan P.
Bioinformatics. 2015 Mar 11. pii: btv144.

Indicspecies 1.7.9 – Studying the Statistical Relationship between Species and groups of sites

Indicspecies 1.7.9

:: DESCRIPTION

Indicspecies‘ is an R package that contains a set of functions to assess the strength of relationship between species and a classification of sites.

::DEVELOPER

Miquel De Cáceres Ainsa

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Windows / Linux
  • R package

:: DOWNLOAD

 Indicspecies

:: MORE INFORMATION

Citation

Improving indicator species analysis by combining groups of sites
Miquel De Cáceres, Pierre Legendre, Marco Moretti
Oikos Volume 119, Issue 10, pages 1674–1684, October 2010

ASAP – Assemble Species by Automatic Partitioning

ASAP

:: DESCRIPTION

ASAP is a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets).

::DEVELOPER

L’Atelier de BioInformatique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Puillandre N, Brouillet S, Achaz G.
ASAP: assemble species by automatic partitioning.
Mol Ecol Resour. 2021 Feb;21(2):609-620. doi: 10.1111/1755-0998.13281. Epub 2020 Nov 20. PMID: 33058550.

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