Online Tools

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

Bio++ development team

0.5.0

under development - Bio++

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

Bio++ development team

1

Bio++ - under development

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

Bio++ development team

1

Bio++ - under development

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

Bio++ development team

1

under development - Bio++

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.

Bio++ development team

1

Bio++ - under development

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.

Bio++ development team

1

Bio++ - under development

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.

Bio++ development team

0.5.0

Bio++ - under development

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

Bio++ development team

0.5.0

Bio++ - under development

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

Bio++ development team

0.5.0

Bio++ - under development

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.

Des Higgins

1.83

Alignment

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.

Julien VEYSSIER, Remy DERNAT, Khalid Belkhir and Philippe GAUBERT

1.1

database

Tool to upload new database versions into DNAbushmeat.

Unknown

1

Compute distance matrix from nucleotide sequences

Felsenstein

3.67

Phylogenetic reconstruction

Online tool for ecceTERA

Edwin Jacox, Celine Scornavacca, Julien Veyssier

1

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

Derrick J. Zwickl

0.96

Phylogenetic reconstruction