CodABC 2.0.0b – Coestimation of Recombination, Substitution and Molecular Adaptation Rates by Approximate Bayesian Computation

CodABC 2.0.0b

:: DESCRIPTION

The package CodABC is computer framework to coestimate Recombination, Substitution and Molecular Adaptation (dN/dS) rates by approximate Bayesian computation from coding sequence alignments.

::DEVELOPER

Dr. MIGUEL ARENAS

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  CodABC

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Apr;32(4):1109-12. doi: 10.1093/molbev/msu411. Epub 2015 Jan 9.
CodABC: A Computational Framework to Coestimate Recombination, Substitution, and Molecular Adaptation Rates by Approximate Bayesian Computation.
Arenas M, Lopes JS, Beaumont MA, Posada D

MassShiftFinder 1.09 – Blind search for Post-translational Modifications and Amino Acid Substitutions

MassShiftFinder 1.09

:: DESCRIPTION

MassShiftFinder is a software tool for doing blind search using peptide mass fingerprints from two proteases with different cleavage specificities. The algorithm relies on overlapping peptides for the two proteases used, and can indicate both modifications and amino acid substitutions. The method can help restrict the area where the modification has occurred.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 MassShiftFinder

:: MORE INFORMATION

Citation

BMC Res Notes. 2008 Dec 19;1:130.
Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases.
Barsnes H, Mikalsen SO, Eidhammer I.

SIFT 6.2.1 – Amino Acid Substitution Affects Protein Function

SIFT 6.2.1

:: DESCRIPTION

SIFT (Sorting Intolerant From Tolerant) is a program for predicting whether an amino acid substitution affects protein function, based on sequence homology and the physical properties of amino acids. It is one of several programs using sequence information for this purpose.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SIFT

:: MORE INFORMATION

Citation:

Ng PC, Henikoff S. 2002.
Accounting for human polymorphisms predicted to affect protein function.
Genome Research 12:436-446. doi:10.1101/gr.212802

MutPred2 – Predicting whether an Amino Acid Substitution in a protein is Deleterious or Neutral

MutPred2

:: DESCRIPTION

MutPred is a web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. In addition, it predicts molecular cause of disease.

::DEVELOPER

MutPred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MutPred2

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 1;25(21):2744-50. doi: 10.1093/bioinformatics/btp528. Epub 2009 Sep 3.
Automated inference of molecular mechanisms of disease from amino acid substitutions.
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P.

MLSTA – Machine Learning Integration for Predicting the Effect of Single Amino Acid Substitutions on Protein Stability

MLSTA

:: DESCRIPTION

MLSTA is a machine learning integration for predicting the effect of single amino acid substitutions on protein stability.

::DEVELOPER

Polymer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Struct Biol. 2009 Oct 19;9:66. doi: 10.1186/1472-6807-9-66.
Machine learning integration for predicting the effect of single amino acid substitutions on protein stability.
Ozen A1, Gönen M, Alpaydan E, Haliloğlu T.

SomaticCall 46233 – Find Substitutions between Sequence Data

SomaticCall 46233

:: DESCRIPTION

SomaticCall is a program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations).

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SomaticCall

:: MORE INFORMATION

InSNP 1.0 – Detect Substitution and Indel SNPs in Sequencing Traces

InSNP 1.0

:: DESCRIPTION

InSNP is a program that detects substitution and indel SNPs in sequencing traces. It uses simple algorithms to detect the mutations and presents the sequences in compact visualizations that let you quickly decide which ones are real.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 InSNP

:: MORE INFORMATION

Citation

Manaster C, Zheng W, Teuber M, W?chter S, D?ring F, Schreiber S, Hampe J (2005).
InSNP: A tool for automated detection and visualization of SNPs and InDels.
Human Mutation 26(1): 11-19