OrthoMaM project

Release v10b (latest)

Requests on 116 species (based on EnsEMBL v91, December 2017, and NCBI, March 2018).
Web interface greatly enhanced

Release v9, April 2015

Requests on 43 species (based on EnsEMBL v79, March 2015).
New species: Papio_anubis, Chlorocebus_sabaeus, Ovis_aries.
Exon detection has been improved.
Raw alignements have been computed with MAFFT.
In this release, we did not exclude alignments which contain sequences leading to very high branch lengths in the corresponding ML phylograms.

Release v8, October 2013

Requests on 40 species (based on EnsEMBL v73, September 2013).
New species: Mustela_putorius_furo.

Release v7, February 2012

Requests on 39 species (based on EnsEMBL v65, December 2011).
New species: Nomascus_leucogenys, Ailuropoda_melanoleuca, Sarcophilus_harrisii.
Sequence alignments have been improved and now rely on MACSE to detect potential frameshifts.
As a consequence alignments may contain the "!" that indicates frameshift events. You can safely replace them by "-" in DNA alignments or by "X" in protein alignments.
Unreliable alignment sites/sequences are removed using trimAl before phylogenetic analyses (raw and filtered alignments are provided).
Exon orthology prediction has been improved and is now based on the corresponding CDS alignments.
Marker detail rendering is now compatible with most web browsers: Firefox, IE, Safari, Chrome (thanks to Benjamin Robert).
A visual rendering of GO annotation is available based on OntoFocus (thanks to Sebastien Harispe).

Release v6, September 2010

Data are the same as in v6a but web interface is improved
There are now two ways to access markers:
- the former textual query form
- a simpler visual way to browse markers
Query results appear in different windows so that query criteria are not lost.
Markers can be queried using any EnsEMBL gene ID (instead of just human ones).
Left menu is simplified (other minor human-computer interaction improvements have been done).

v6a, July 2010

Requests on 36 species (based on EnsEMBL v56, September 2009).
New species: Callithrix_jacchus, Sus_scrofa, Macropus_eugenii.
Queries can now be done using a list of human gene EnsEMBL identifiers (or gene symbols).
Maximum likelihood (ML) trees can be downloaded.
Thousands of files can now be downloaded at once instead of 100 in previous versions.
A bug about GO annotation rendering has been fixed.

Release v5, October 2009

Requests on 33 species (based on EnsEMBL v54, May 2009).
New species: Gorilla_gorilla, Tarsius_syrichta, Dipodomys_ordii, Vicugna_pacos, Tursiops_truncatus, Pteropus_vampyrus, Procavia_capensis, Choloepus_hoffmanni.
Exons / CDS can be queried according to a list of species required.
Markers can be queried based on the corresponding human gene EnsEMBL identifier.
Gene annotations are now available for each marker (human gene description and gene ontology [GO] terms).
Phylogenetic trees readability is enhanced by taxonomic coloring.

Release v4, July 2008

Requests on 25 taxa (based on EnsEMBL v49, March 2008)
This version includes both CDS and exon data.
Query results can now be sorted according to descriptors and downloaded as zip archives.
The average responsivness of the web server has been significantly improved.

Release v3, May 2008

Requests on 25 taxa (based on EnsEMBL v49, March 2008)
New species: Pongo_pygmaeus, Equus_caballus.
We found and corrected a bug in previous versions that, in very few alignments, led us to propose some non orthologous sequences.

Release v2, March 2008

Requests on 23 taxa (based on EnsEMBL v48, December 2007)
New species: Otolemur_garnettii, Microcebus_murinus, Tupaia_belangeri, Cavia_porcellus, Spermophilus_tridecemlineatus (= Ictidomys), Ochotona_princeps, Felis_catus, Myotis_lucifugus, Erinaceus_europaeus, Sorex_araneus, Ornithorhynchus_anatinus.
Amino acid alignments are provided.
A dedicated web server is used for this project.
Due to web connection trouble, some chromosomes were not completely analysed. Some markers were thus missing.

Release v1, July 2007

Requests on 12 taxa (based on EnsEMBL v41, October 2006)
Species list: Homo_sapiens, Pan_troglodytes, Macaca_mulatta, Mus_musculus, Rattus_norvegicus, Oryctolagus_cuniculus, Bos_taurus, Canis_familiaris, Dasypus_novemcinctus, Loxodonta_africana, Echinops_telfairi, Monodelphis_domestica.

Release v10b (latest)	Requests on 116 species (based on EnsEMBL v91, December 2017, and NCBI, March 2018). Web interface greatly enhanced
Release v9, April 2015	Requests on 43 species (based on EnsEMBL v79, March 2015). New species: Papio_anubis, Chlorocebus_sabaeus, Ovis_aries. Exon detection has been improved. Raw alignements have been computed with MAFFT. In this release, we did not exclude alignments which contain sequences leading to very high branch lengths in the corresponding ML phylograms.
Release v8, October 2013	Requests on 40 species (based on EnsEMBL v73, September 2013). New species: Mustela_putorius_furo.
Release v7, February 2012	Requests on 39 species (based on EnsEMBL v65, December 2011). New species: Nomascus_leucogenys, Ailuropoda_melanoleuca, Sarcophilus_harrisii. Sequence alignments have been improved and now rely on MACSE to detect potential frameshifts. As a consequence alignments may contain the "!" that indicates frameshift events. You can safely replace them by "-" in DNA alignments or by "X" in protein alignments. Unreliable alignment sites/sequences are removed using trimAl before phylogenetic analyses (raw and filtered alignments are provided). Exon orthology prediction has been improved and is now based on the corresponding CDS alignments. Marker detail rendering is now compatible with most web browsers: Firefox, IE, Safari, Chrome (thanks to Benjamin Robert). A visual rendering of GO annotation is available based on OntoFocus (thanks to Sebastien Harispe).
Release v6, September 2010	Data are the same as in v6a but web interface is improved There are now two ways to access markers: the former textual query form a simpler visual way to browse markers Query results appear in different windows so that query criteria are not lost. Markers can be queried using any EnsEMBL gene ID (instead of just human ones). Left menu is simplified (other minor human-computer interaction improvements have been done).
v6a, July 2010	Requests on 36 species (based on EnsEMBL v56, September 2009). New species: Callithrix_jacchus, Sus_scrofa, Macropus_eugenii. Queries can now be done using a list of human gene EnsEMBL identifiers (or gene symbols). Maximum likelihood (ML) trees can be downloaded. Thousands of files can now be downloaded at once instead of 100 in previous versions. A bug about GO annotation rendering has been fixed.
Release v5, October 2009	Requests on 33 species (based on EnsEMBL v54, May 2009). New species: Gorilla_gorilla, Tarsius_syrichta, Dipodomys_ordii, Vicugna_pacos, Tursiops_truncatus, Pteropus_vampyrus, Procavia_capensis, Choloepus_hoffmanni. Exons / CDS can be queried according to a list of species required. Markers can be queried based on the corresponding human gene EnsEMBL identifier. Gene annotations are now available for each marker (human gene description and gene ontology [GO] terms). Phylogenetic trees readability is enhanced by taxonomic coloring.
Release v4, July 2008	Requests on 25 taxa (based on EnsEMBL v49, March 2008) This version includes both CDS and exon data. Query results can now be sorted according to descriptors and downloaded as zip archives. The average responsivness of the web server has been significantly improved.
Release v3, May 2008	Requests on 25 taxa (based on EnsEMBL v49, March 2008) New species: Pongo_pygmaeus, Equus_caballus. We found and corrected a bug in previous versions that, in very few alignments, led us to propose some non orthologous sequences.
Release v2, March 2008	Requests on 23 taxa (based on EnsEMBL v48, December 2007) New species: Otolemur_garnettii, Microcebus_murinus, Tupaia_belangeri, Cavia_porcellus, Spermophilus_tridecemlineatus (= Ictidomys), Ochotona_princeps, Felis_catus, Myotis_lucifugus, Erinaceus_europaeus, Sorex_araneus, Ornithorhynchus_anatinus. Amino acid alignments are provided. A dedicated web server is used for this project. Due to web connection trouble, some chromosomes were not completely analysed. Some markers were thus missing.
Release v1, July 2007	Requests on 12 taxa (based on EnsEMBL v41, October 2006) Species list: Homo_sapiens, Pan_troglodytes, Macaca_mulatta, Mus_musculus, Rattus_norvegicus, Oryctolagus_cuniculus, Bos_taurus, Canis_familiaris, Dasypus_novemcinctus, Loxodonta_africana, Echinops_telfairi, Monodelphis_domestica.