Online tools

Results

Query : Alignment [subsection]

Online Tools (10)

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


Gblocks

Alignment

 

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Author(s)

Jose Castresana


Version

1


Subsections

Alignment


MAFFT

Alignment

 

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of

Author(s)

Kazutaka Katoh


Version

6.814b


Subsections

Alignment


Multiple alignment of protein-coding DNA sequences : Facilitates the multiple alignment of protein-coding DNA sequences by aligning the amino acids sequences they specify.

Author(s)

Bininda-Emonds


Version

1


Subsections

Tool - Alignment


MACSE

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 0.9b1

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

0.9b1


Subsections

Alignment


Megablast

Alignment

 

Mega BLAST uses a greedy algorithm [1] for the nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used (see explanation below), it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the blastn program of traditional BLAST algorithm.

Author(s)

NCBI -Tao Tao


Version

1


Subsections

Alignment - Blast


1 -> Alignment (ClustalW / Mafft / Muscle)
2 -> Gblocks
3 -> Phylogenetic reconstruction (Phyml / RaxML HPC MPI / MrBayes)
Under developement

Author(s)

MBB development Team


Version

0.0


Subsections

Pipeline - Phylogenetic reconstruction - Alignment


MACSE V1

Alignment

 

Citation: Ranwez V, Harispe S, Delsuc F, Douzery EJP (2011) MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons. PLoS ONE 6(9): e22594. doi:10.1371/journal.pone.0022594

corresponding author: vincent.ranwez@supagro.inra.fr

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.

We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

MACSE is distributed as an open-source java file executable with freely available source code and can be used via this web interface.

Online Tool version : 1.01b

This Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page
N.B.: online access to this tool is limited (details here)

Check latest release, MACSE version (1.01b). executable (jar file) with source code here .

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel J. P. DOUZERY


Version

1.01b


Subsections

Alignment


IDxen upload

Alignment

 

Tool to upload new reference versions to IDxen.

Author(s)

Julien Veyssier


Version

1


Subsections

Alignment - Phylogenetic reconstruction - Pipeline - Tool


Softwares (1)

MACSE

Alignment

  

NEW MACSE version (1.01b)

MACSE now provides a full toolkit dedicated to coding sequence alignments. This toolkit allows us to reliably align thousands of COI and matK sequences in a barcoding context (see our barcoding subproject web page for further information). Here are some of the functionalities provided by the various subprograms included in MACSE: Enriching an existing alignment with additional sequences Refining an existing alignment Splitting an existing alignment keeping a subset of sites and/or sequences Formatting and exporting an alignment (e.g. by removing or masking codons containing frameshifts) Translating a nucleotide alignment into an amino acid alignment ... For usage examples see MACSE tutorial and download associated examples.
Source code of MACSE can be downloaded, using the svn facilities of redmine with the following command line and "guest" as login and password: svn checkout http://kimura.univ-montp2.fr/svn/macse
project web page: MACSE Webpage

corresponding author: vincent.ranwez@supagro.inra.fr

Author(s)

Vincent RANWEZ, Sebastien HARISPE, Frederic DELSUC, Emmanuel DOUZERY


Version

1.01b


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Subsections

Alignment




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