Online tools Phylogenomics

Online Tools

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Gblocks

Alignment

 

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Author(s)

Jose Castresana


Version

1


Subsections

Alignment


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IDxen

Pipeline

 

IDxen : EPA on mitochondrial reads.

Author(s)

Julien Veyssier


Version

1


Subsections

Pipeline - Tool


IDxen upload

Alignment

 

Tool to upload new reference versions to IDxen.

Author(s)

Julien Veyssier


Version

1


Subsections

Alignment - Phylogenetic reconstruction - Pipeline - Tool


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MACSE

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 0.9b1

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

0.9b1


Subsections

Alignment


MACSE V1

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 1.01b

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

1.01b


Subsections

Alignment


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MAFFT

Alignment

 

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of

Author(s)

Kazutaka Katoh


Version

6.814b


Subsections

Alignment


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MrBayes

Phylogenetic reconstruction

 

Bayesian Inference for Phylogeny

Author(s)

J. P. Huelsenbeck, F. Ronquist


Version

3.1.2


Subsections

Phylogenetic reconstruction


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MrBayes MCMC convergence plotter

Phylogenetic reconstruction

 

A visual tool to diagnose the convergenge of MrBayes MCMCM

Author(s)

Khalid Belkhir


Version

1


Subsections

Phylogenetic reconstruction


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MRtools is a JAVA 1.6 software that is dedicated to the building of binary representation of a collection of phylogenetic trees.
Three binary coding are available: bipartition- (Baum 1992; Ragan 1992; see also Doyle 1992), triplet- (Nelson and Ladiges 1994; Williams and Humphries 2003; Wilkinson et al. 2004), and quartet-based binary matrix representation. Matrix representations are outputed in NEXUS format, with the possibility to include an 'ASSUMPTIONS' block in order to reduce the size of the binary matrix representation, which is often large and redondant when the triplet- and quartet-based binary coding are used (Ranwez et al. 2010). Moreover, as these two last coding induce redondant information for each input tree (Dekker 1986; Wilkinson et al. 2004), MRtools is able to compute the minimum set of binary characters that entail each input tree (e.g. one per internal branch for a fully resolved tree; Steel 1992). Finally, MRtools implements a very fast heuristics to infer a supertree from the so-built binary matrix representation. As each internal branch of a supertree corresponds to a bipartition-based binary character, confidence value is also computed for each internal brach by computing the proportion of binary characters in the matrix representation that are compatible with the bipartition-based binary character induced by the given branch.

Author(s)

Alexis Criscuolo


Version

1


Tags

under development


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Neighbor

Phylogenetic reconstruction

 

Neighbor-Joining and UPGMA methods

Author(s)

Felsenstein


Version

3.67


Subsections

Phylogenetic reconstruction


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PAUP

Phylogenetic reconstruction

 

PAUP is the most widely used package for phylogenetic inference, and now implements

Author(s)

swofford


Version

4


Subsections

Phylogenetic reconstruction


Tags

under development


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1 -> Alignment (ClustalW / Mafft / Muscle)
2 -> Gblocks
3 -> Phylogenetic reconstruction (Phyml / RaxML HPC MPI / MrBayes)
Under developement

Author(s)

MBB development Team


Version

0.0


Subsections

Pipeline - Phylogenetic reconstruction - Alignment


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PhyML

Phylogenetic reconstruction

 

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

Author(s)

S. Guindon and O. Gascuel


Version

3.0


Subsections

Phylogenetic reconstruction


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Popphyl pipeline

Author(s)

MBB developpers


Version

1


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Program to compute distance matrix from protein sequences

Author(s)

Felsenstein


Version

3.67


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