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BppAncestor |
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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
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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
Bio++ development team
1
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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
Bio++ development team
1
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Parsimony analyses. Tree optimization using Nearest Neighbor Interchanges (NNI) movements Non-parametric bootstrap
Author(s)Bio++ development team
1
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BppPhySamp |
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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.
Bio++ development team
1
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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.
Bio++ development team
1
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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.
Bio++ development team
0.5.0
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Sequence file manipulation.
Read / Write to all format available in Bio++
Perform translation, transcription, replication, of sequences.
Bio++ development team
0.5.0
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BppTreeDraw |
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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
0.5.0
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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
1.83
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DNAbushmeat |
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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
DNAbushmeat_upload |
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Tool to upload new database versions into DNAbushmeat.
Author(s)Unknown
1
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Compute distance matrix from nucleotide sequences
Author(s)Felsenstein
3.67
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Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion
Author(s)Derrick J. Zwickl
0.96
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