Online tools Phylogenomics

Online Tools

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Ancestral sequences reconstruction under various models.
Substitution models: same as BppML and BppSeqGen, including covarion and non-homogeneous models.

Author(s)

Bio++ development team


Version

0.5.0


Tags

under development - Bio++


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Distance matrix estimation and tree reconstruction, under various protein and nucleotides models.
Distance estimation (maximum likelihood)
Tree reconstruction: U/W PGMA, Neighbor Joining, BioNJ
Substitution models: JC69, K80, HKY85, T92, GTR, JTT92, and more
Gamma distribution of rates
Covarions models
Iterative approach to estimate non-topological parameters
Non-parametric bootstrap and approximation

Author(s)

Bio++ development team


Version

1


Tags

Bio++ - under development


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Maximum likelihood analyses.
Substitution models: JC69, K80, HKY85, T92, GTR, JTT92, and more, including protein and codon models.
Gamma distribution (+ invariant) of rates
Covarions models
Non homogeneous models, with a very general syntax supporting virtually any possible model.
Parameter estimation with various algorithms
Tree optimization using Nearest Neighbor Interchanges (NNI) movements
Non-parametric bootstrap
Site specific rate estimation

Author(s)

Bio++ development team


Version

1


Tags

Bio++ - under development


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Parsimony analyses. Tree optimization using Nearest Neighbor Interchanges (NNI) movements Non-parametric bootstrap

Author(s)

Bio++ development team


Version

1


Tags

under development - Bio++


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Phylogenetic sequences sampler.
Sample sequences from a file, according to a phylogenetic tree or a distance matrix and a user-specified threshold. Keep only one sequence (the longest, or randomly) within clusters of sequences with a distance lower than the threshold.

Author(s)

Bio++ development team


Version

1


Tags

Bio++ - under development


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Serial re-rooting of trees.
Takes a list of trees as input, and a list of taxa to serve as outgroup. Re-root all the trees in the list according to the specified outgroups.

Author(s)

Bio++ development team


Version

1


Tags

Bio++ - under development


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Sequence simulation (parametric bootstrap).
Substitution models: JC69, K80, HKY85, T92, GTR, JTT92, and more, including protein and codon models.
Gamma (+ invariants) distribution of rates
Covarions models
Non homogeneous models, with a very general syntax supporting virtually any possible model.

Author(s)

Bio++ development team


Version

0.5.0


Tags

Bio++ - under development


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Sequence file manipulation.
Read / Write to all format available in Bio++
Perform translation, transcription, replication, of sequences.

Author(s)

Bio++ development team


Version

0.5.0


Tags

Bio++ - under development


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Drawing phylogenetic trees. Plot a tree to a file in vector format, so that it can easily be edited afterwards.

Author(s)

Bio++ development team


Version

0.5.0


Tags

Bio++ - under development


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ClustalW

Alignment

 

ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

Author(s)

Des Higgins


Version

1.83


Subsections

Alignment


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DNAbushmeat

database

 

DNA-typing of African forest bushmeat.

The bushmeat trade in tropical Africa represents illegal, unsustainable off-takes of millions of tons of wild game —mostly mammals— per year. Because the bushmeat items sold on markets may consist of unrecognizable pieces of processed meat, we provide a species-identification genetic tool based on ‘forensically informative nucleotide sequencing’ (FINS) to complement standard bushmeat surveys. Our expert-curated nucleotide datasets shall be progressively fed to become a reference frame for the DNA-typing of African forest bushmeat.

Author(s)

Julien VEYSSIER, Remy DERNAT, Khalid Belkhir and Philippe GAUBERT


Version

1.1


Subsections

database


Tool to upload new database versions into DNAbushmeat.

Author(s)

Unknown


Version

1


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DNAdist

Phylogenetic reconstruction

 

Compute distance matrix from nucleotide sequences

Author(s)

Felsenstein


Version

3.67


Subsections

Phylogenetic reconstruction


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Online tool for ecceTERA

Author(s)

Edwin Jacox, Celine Scornavacca, Julien Veyssier


Version

1


Garli

Phylogenetic reconstruction

 

Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion

Author(s)

Derrick J. Zwickl


Version

0.96


Subsections

Phylogenetic reconstruction


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