BAli-Phy 3.6.0 – Bayesian Alignment and Phylogeny estimation

BAli-Phy 3.6.0

:: DESCRIPTION

BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.

::DEVELOPER

BAli-Phy team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows

:: DOWNLOAD

 BAli-Phy

:: MORE INFORMATION

Citation

Suchard MA and Redelings BD
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny,
Bioinformatics, 22:2047-2048, 2006.

CEM 0.9.1 – Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads

CEM 0.9.1

:: DESCRIPTION

CEM is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 CEM

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2914-21. doi: 10.1093/bioinformatics/bts559. Epub 2012 Oct 11.
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
Li W1, Jiang T.

CoNCoS 0.2 – Copy Number Estimation with Controlled Support

CoNCoS 0.2

:: DESCRIPTION

CoNCoS is a tool for researchers concerned with copy number estimation from next-generation sequencing data.It detects copy number aberrations and outputs a list composed of their position, copy number and affected gene(s).

::DEVELOPER

CoNCoS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • JRE

:: DOWNLOAD

 CoNCoS

:: MORE INFORMATION

Citation

CoNCoS: Copy number estimation in cancer with controlled support.
Abdallah AT, Fischer M, Nürnberg P, Nothnagel M, Frommolt P.
J Bioinform Comput Biol. 2015 Sep 4:1550027.

Psafe 20120530 – Pooled Sequencing Allele Frequency Estimation

Psafe 20120530

:: DESCRIPTION

Psafe is a pipeline to adjust the biases and errors of sequencing data to gain more accurate allele frequency estimation.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • Perl

:: DOWNLOAD

 Psafe

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 Sep;36(6):549-60. doi: 10.1002/gepi.21648. Epub 2012 Jun 6.
Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples.
Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H.

LDhelmet 1.10 – Fine-scale Recombination Rate Estimation

LDhelmet 1.10

:: DESCRIPTION

LDhelmet is a software program for statistical inference of fine-scale crossover recombination rates from population genetic data.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 LDhelmet

:: MORE INFORMATION

Citation

Chan, A.H., Jenkins, P.A., and Song, Y.S.
Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.
PLoS Genetics, vol. 8 no. 12 (2012) e1003090.

influx_s 5.4.0 – Estimation of Metabolic Fluxes and Metabolite Concentrations

influx_s 5.4.0

:: DESCRIPTION

influx_s is a scientific software for estimation of metabolic fluxes and metabolite concentrations in a stationary framework.

::DEVELOPER

MetaSys

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsx
  • R
  • Python

:: DOWNLOAD

 influx_s

:: MORE INFORMATION

Citation

influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labeling experiments
Serguei Sokol, Pierre Millard and Jean-Charles Portais
Bioinformatics 2012 Mar 1;28(5):687-93

stochprofML 2.0.3 – Stochastic Profiling using Maximum Likelihood Estimation

stochprofML 2.0.3

:: DESCRIPTION

stochprofML is an R package of parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

::DEVELOPER

Biostatistics, Institute of Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
:: DOWNLOAD

 stochprofML

:: MORE INFORMATION

Citation:

Amrhein L, Fuchs C.
stochprofML: stochastic profiling using maximum likelihood estimation in R.
BMC Bioinformatics. 2021 Mar 15;22(1):123. doi: 10.1186/s12859-021-03970-7. PMID: 33722188; PMCID: PMC7958472.

mhsmm 0.4.16 – Parameter Estimation and Prediction for Hidden Markov and semi-Markov models for data with multiple Observation Sequences

mhsmm 0.4.16

:: DESCRIPTION

mhsmm is a software of parameter estimation and prediction for hidden Markov and semi-Markov models for data with multiple observation sequences. The software is suitable for equidistant time series data, with multivariate and/or missing data.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

  mhsmm

:: MORE INFORMATION

Citation

Jared O’Connell, Soren Hojsgaard (2011).
Hidden Semi Markov Models for Multiple Observation Sequences: The mhsmm Package for R.
Journal of Statistical Software, 39(4), 1-22.

Phylonium 1.4 – Fast and Accurate Estimation of Evolutionary Distances

Phylonium 1.4

:: DESCRIPTION

Phylonium is a program for estimating the evolutionary distances between closely related genomes. It is much faster than alignment based approaches for phylogeny reconstruction and usually more accurate than competing alignment-free methods.

::DEVELOPER

Fabian Klötzl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Phylonium

:: MORE INFORMATION

Citation

Klötzl F, Haubold B.
Phylonium: fast estimation of evolutionary distances from large samples of similar genomes.
Bioinformatics. 2020 Apr 1;36(7):2040-2046. doi: 10.1093/bioinformatics/btz903. PMID: 31790149; PMCID: PMC7141870.