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ABCreg implements the linear regression approach to "Approximate Bayesian Computation" ...

Author(s)

Kevin Thornton


Version

1


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ABySS

Assembler

 

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. We propose MPI version using 4 cores on the platform.

Author(s)

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ


Version

1.2.1


Subsections

Assembler


Tags

parallel - De novo


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AFCR

Tool

 

This procedure is aimed to reduce the dimensionality of a genotypic data to visualize them in a subspace of 2 or 3 dimensions. Adapted from ca R-package by Nenadic and Greenacre.

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


AFCRPOP

Tool

 

This procedure is aimed to reduce the dimensionality of a genotypic data to visualize them in a subspace of 2 or 3 dimensions. Adapted from ca R-package by Nenadic and Greenacre. Pseudo-individus are constructed for each population by summing individual alleles counts. These values are then added to the matrix of individual alleles and analysed with ca() while setting only the pseudo-individus as active elements.

Author(s)

Unknown


Version

1


Subsections

Tool


After read cleaning this pipeline will call Abyss for denovo assembly in contigs. The resulting contigs can be further assembled with CAP3. The contigs are then blasted against a provided multi-fasta file and/or ncbi databases. If a blastx on nr is chosen the result can be used to annotate the best hits with blast2go.

Author(s)

MBB dev


Version

1


Subsections

Pipeline - Blast - Assembler


Tags

De novo


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AAA sssss aaa

Author(s)

Khalid


Version

1


Subsections

Pipeline - Assembler


Tags

De novo


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Bl2seq

Blast

 

The program bl2seq is designed to compare two input FASTA sequences directly bypassing the formatdb step. This allows users to quickly assess the similarities between two input sequences. The program is capable of performing six types of blast searches: blastn, blastp, blastx, tblastn, tblastx, and megabalst in place of blastn.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman


Version

1


Subsections

Blast


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Used in order to build a database on a given sequence file and perform a Blast on it. Useful to realize reciprocal Blast. The proposed version of formatDB and Blast are those including MPI compatibility. Then each execution use 8 cores to reduce execution time.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman ... [wrapper : MBB development team]


Version

1


Subsections

Blast


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BLAST2

Blast

 

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman


Version

2


Subsections

Blast


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Perform blast X on Nucleotidic sequences in order to extract GO terms associated. Use blast2 with blastX program to retrieve XML formated results then launch b2g4pipe using Gene Ontology (assocdb-data 2010-12).

Optionally accepts XML blast result to avoid the blastX on NCBI NR database step.

Author(s)

MBB development team


Version

2


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BLASTClust is a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. The program begins with pairwise matches and places a sequence in a cluster if the sequence matches at least one sequence already in the cluster. In the case of proteins, the blastp algorithm is used to compute the pairwise matches; in the case of nucleotide sequences, the Megablast algorithm is used.

Author(s)

Ilya Dondoshansky, Yuri Wolf


Version

2.2.21


Subsections

Blast


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Bowtie

Mapping

 

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Author(s)

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast


Version

0.12.5


Subsections

Mapping


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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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Co-dominant Markers pair-wise genetic distances.

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


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