pfilt 1.5 – Sequence Filtering for Low-complexity, Coiled-coil and Biased Amino Acid Regions

pfilt 1.5

:: DESCRIPTION

pfilt program is designed to mask out (i.e. replace amino acid characters with Xs) regions of low complexity, coiled-coil regions and regions with extremely biased amino acid compositions. For compositional biased regions,only the overrepresented amino acids are masked.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  pfilt

:: MORE INFORMATION

Citation:

Jones, D.T. & Swindells, M.B. (2002)
Getting the most from PSI-BLAST.
Trends Biochem Sci. 2002 Mar;27(3):161-4.

rate4site 2.01 – Detect Conserved Amino-acid Site

rate4site 2.01

:: DESCRIPTION

rate4site is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in a multiple sequence alignment.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  rate4site

:: MORE INFORMATION

Citation

Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T. 2004.
Comparison of site-specific rate-inference methods: Bayesian methods are superior.
Mol Biol Evol 21: 1781-1791.

PutGaps Beta – DNA Gapped File from Amino Acid Alignment

PutGaps Beta

:: DESCRIPTION

PutGaps is a software to add gaps to a DNA alignment file based on its Amino Acid equivalent.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

PutGaps

:: MORE INFORMATION

ModelGenerator 0.851 – Amino Acid & Nucleotide Substitution Model Selection

ModelGenerator 0.851

:: DESCRIPTION

ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

ModelGenerator

:: MORE INFORMATION

Citation:

Thomas M Keane, Christopher J Creevey ,Melissa M Pentony, Thomas J Naughton and James O McInerney (2006)
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified,
BMC Evolutionary Biology, 6:29

Wregex 2.1 – Amino Acid Motif searching

Wregex 2.1

:: DESCRIPTION

Wregex (weighted regular expression).is a software tool for amino acid motif searching.

::DEVELOPER

EhuBio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Wregex

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1220-7. doi: 10.1093/bioinformatics/btu016. Epub 2014 Jan 9.
Prediction of nuclear export signals using weighted regular expressions (Wregex).
Prieto G1, Fullaondo A, Rodriguez JA.

AIS – Classify Amino Acids

AIS

:: DESCRIPTION

AIS (Almost Invariant Sets) is a program which uses a novel criterion and method to classify amino acids. The goal is to identify sets of amino acids with a high probability of change between elements of the set but small probability of change between different sets by using amino acid replacement matrices and their eigenvectors. After identification of the subsets the quality of the partition is assessed with a conductance measure

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AIS

:: MORE INFORMATION

Citation:

Kosiol et al. (2004),
A new criterion and method for amino acid classification
Journal of Theoretical Biology 228:97-106.

TreeSAAP 3.2 – Selection of Amino Acid Properties using Phylogenetic Trees model

TreeSAAP 3.2

:: DESCRIPTION

TreeSAAP (Selection of Amino Acid Properties Based on Phylogenetic Trees) measures the selective influences on 31 structural and biochemical amino acid properties during phylogenesis (the history of genealogical development) and performs goodness-of-fit and categorical statistical tests.

::DEVELOPER

McClellan, David

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

TreeSAAP

:: MORE INFORMATION

Citation

TreeSAAP: selection on amino acid properties using phylogenetic trees.
Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA.
Bioinformatics. 2003 Mar 22;19(5):671-2

FastMG 20140909 – Estimate Amino Acid Substitution Matrices for large data sets

FastMG 20140909

:: DESCRIPTION

FastMG is simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 FastMG

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Oct 24;15:341. doi: 10.1186/1471-2105-15-341.
FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.
Dang CC, Le VS, Gascuel O, Hazes B, Le QS

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.

NIAS-Server 1.0 – Neighbors Influence of Amino acids and Secondary Structures in Proteins

NIAS-Server 1.0

:: DESCRIPTION

NIAS is a server to help the analysis of the conformational preferences of amino acid residues in proteins.

::DEVELOPER

SBCB – Structural Bioinformatics and Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Borguesan, B.; Inostroza-Ponta, M.; Dorn, M.
NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.
Journal of Computational Biology. March 2017, 24(3): 255-265.