FastME 2.1.5 – Fast & Accurate Phylogeny Reconstruction

FastME 2.1.5

:: DESCRIPTION

FastME is a software for fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. FastME showed better topological accuracy than NJ, BIONJ, WEIGHBOR and FITCH, in all evolutionary conditions we tested, which include large range deviations from molecular clock and substitution rates. When the number of taxa is high, its superiority over NJ, BIONJ and WEIGHBOR becomes important, while FITCH remains close to FastME but becomes hard to use due to its slowness. FastME is very fast, even faster than NJ, and can easily be applied to very large data sets (> 1000 taxa).

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

FastME

:: MORE INFORMATION

Citation

Mol Biol Evol. 2015 Oct;32(10):2798-800. doi: 10.1093/molbev/msv150. Epub 2015 Jun 30.
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.
Lefort V, Desper R, Gascuel O

Desper R., Gascuel O.
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
Journal of Computational Biology. 2002 9(5):687-705.

ACANA – Accurate and Consistent Alignment Tool for DNA sequences

ACANA

:: DESCRIPTION

ACANA  (ACcurate ANchoring Alignment)) is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.

::DEVELOPER

ACANA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX

:: DOWNLOAD

 ACANA

:: MORE INFORMATION

Citation

Weichun Huang, David M. Umbach, and Leping Li,
Accurate anchoring alignment of divergent sequences.
Bioinformatics 22:29-34, Jan 1 2006

PSICOV 2.13 – Accurate Contact Prediction from Large Protein Alignments

PSICOV 2.13

:: DESCRIPTION

PSICOV introduces the use of sparse inverse covariance estimation to the problem of protein contact prediction. The method builds on work which had previously demonstrated corrections for phylogenetic and entropic correlation noise and allows accurate discrimination of direct from indirectly coupled mutation correlations in the MSA.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PSICOV

:: MORE INFORMATION

Citation:

David T. Jones, Daniel W. A. Buchan, Domenico Cozzetto and Massimiliano Pontil
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
Bioinformatics (2012) 28 (2): 184-190.

SNPdetector 3 – Sensitive and Accurate SNP Detection

SNPdetector 3

:: DESCRIPTION

SNPdetector is a software for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool), and independent genotype assays in three large-scale investigations.

::DEVELOPER

Jinghui Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SNPdetector

:: MORE INFORMATION

Citation

Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, et al. (2005)
SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection.
PLoS Comput Biol 1(5): e53.

GAAS 0.17 – Calculate Accurate Community Composition and Average Genome Size

GAAS 0.17

:: DESCRIPTION

GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.

::DEVELOPER

Florent E. Angly (florent.angly@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GAAS

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2009 Dec;5(12):e1000593. Epub 2009 Dec 11.
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.
Angly FE , et al.

MSAProbs 0.9.7 – Parallel and Accurate Multiple Sequence Alignment

MSAProbs 0.9.7

:: DESCRIPTION

MSAProbs is a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MSAProbs

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities“.
Bioinformatics, 2010, 26(16): 1958 -1964