Online tools

Online Tools

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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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Co-dominant Markers permutation on pair-wise distances.

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


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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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BWA Sampe

Mapping

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Mapping - Assembler


Tags

bwa


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BWA Samse

Assembler

 

Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Please see the BWA manual page for more information.

Author(s)

Heng Li, Chi-Kwong Wong


Version

0.5.8


Subsections

Assembler - Mapping


Tags

bwa


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CAP3

Assembler

 

The program has a capability to clip 5′ and 3′ low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward–reverse constraints to correct assembly errors and link contigs.

Author(s)

Huang, X. and Madan, A.


Version

1


Subsections

Assembler


Tags

under development


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First cfit online tool

Author(s)

Unknown


Version

1


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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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Pipeline for de Novo assembly of reads from a mix of 454 and Illumina sequencing technologies.

Author(s)

Vincent Cahais


Version

1


Tags

under development


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Cufflinks

Expression

 

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

Author(s)

Cole Trapnell et al.


Version

0.9.2


Subsections

Expression


Tags

RNA-seq


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