Construction of Phylogenetic Trees on Parallel Clusters
Identifieur interne : 000F11 ( France/Analysis ); précédent : 000F10; suivant : 000F12Construction of Phylogenetic Trees on Parallel Clusters
Auteurs : Frédéric Guinand [Allemagne, France] ; Gilles Parmentier [France] ; Denis Trystram [France]Source :
- Lecture Notes in Computer Science [ 0302-9743 ] ; 2006.
Abstract
Abstract: In this work, we present the preliminary step of a novel approach for the construction of phylogenetic trees on large parallel clusters of PCs. Computation of multiple alignments of biological sequences and phylogenetic tree construction are performed simultaneously. Any algorithm built upon this process uses the concept of neighborhood (which can be informally defined as sets of evolutionary related sequences). The process, called PhylTre, schematically consists in three iterative steps: the first step produces an undirected graph from a pre-processing operation. The second step aims at determining a neighborhood for each sequence. The third step builds partial phylogenetic trees using results stemmed from step two. The steps are applied iteratively until the whole phylogenetic tree is obtained. A sequential code is available and it is currently implemented in parallel on a large cluster of PCs available at ID-IMAG.
Url:
DOI: 10.1007/3-540-48086-2_24
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000B91
- to stream Istex, to step Curation: 000B91
- to stream Istex, to step Checkpoint: 000747
- to stream Main, to step Merge: 001649
- to stream Main, to step Curation: 001608
- to stream Main, to step Exploration: 001608
- to stream France, to step Extraction: 000F11
Links to Exploration step
ISTEX:52262FCF32545C90BD62024AB5E06B622D4A16A2Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Construction of Phylogenetic Trees on Parallel Clusters</title><author><name sortKey="Guinand, Frederic" sort="Guinand, Frederic" uniqKey="Guinand F" first="Frédéric" last="Guinand">Frédéric Guinand</name></author><author><name sortKey="Parmentier, Gilles" sort="Parmentier, Gilles" uniqKey="Parmentier G" first="Gilles" last="Parmentier">Gilles Parmentier</name></author><author><name sortKey="Trystram, Denis" sort="Trystram, Denis" uniqKey="Trystram D" first="Denis" last="Trystram">Denis Trystram</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:52262FCF32545C90BD62024AB5E06B622D4A16A2</idno><date when="2002" year="2002">2002</date><idno type="doi">10.1007/3-540-48086-2_24</idno><idno type="url">https://api.istex.fr/document/52262FCF32545C90BD62024AB5E06B622D4A16A2/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000B91</idno><idno type="wicri:Area/Istex/Curation">000B91</idno><idno type="wicri:Area/Istex/Checkpoint">000747</idno><idno type="wicri:doubleKey">0302-9743:2002:Guinand F:construction:of:phylogenetic</idno><idno type="wicri:Area/Main/Merge">001649</idno><idno type="wicri:Area/Main/Curation">001608</idno><idno type="wicri:Area/Main/Exploration">001608</idno><idno type="wicri:Area/France/Extraction">000F11</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Construction of Phylogenetic Trees on Parallel Clusters</title><author><name sortKey="Guinand, Frederic" sort="Guinand, Frederic" uniqKey="Guinand F" first="Frédéric" last="Guinand">Frédéric Guinand</name><affiliation wicri:level="1"><country xml:lang="fr">Allemagne</country><wicri:regionArea>LIH - Le Havre University Frederic</wicri:regionArea></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation></author><author><name sortKey="Parmentier, Gilles" sort="Parmentier, Gilles" uniqKey="Parmentier G" first="Gilles" last="Parmentier">Gilles Parmentier</name><affiliation wicri:level="1"><country xml:lang="fr">France</country><wicri:regionArea>ID-IMAG Grenoble</wicri:regionArea></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation></author><author><name sortKey="Trystram, Denis" sort="Trystram, Denis" uniqKey="Trystram D" first="Denis" last="Trystram">Denis Trystram</name><affiliation wicri:level="1"><country xml:lang="fr">France</country><wicri:regionArea>ID-IMAG Grenoble</wicri:regionArea></affiliation><affiliation wicri:level="1"><country wicri:rule="url">France</country></affiliation></author></analytic><monogr></monogr><series><title level="s">Lecture Notes in Computer Science</title><imprint><date>2006</date></imprint><idno type="ISSN">0302-9743</idno><idno type="ISSN">0302-9743</idno></series><idno type="istex">52262FCF32545C90BD62024AB5E06B622D4A16A2</idno><idno type="DOI">10.1007/3-540-48086-2_24</idno><idno type="ChapterID">24</idno><idno type="ChapterID">Chap24</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0302-9743</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: In this work, we present the preliminary step of a novel approach for the construction of phylogenetic trees on large parallel clusters of PCs. Computation of multiple alignments of biological sequences and phylogenetic tree construction are performed simultaneously. Any algorithm built upon this process uses the concept of neighborhood (which can be informally defined as sets of evolutionary related sequences). The process, called PhylTre, schematically consists in three iterative steps: the first step produces an undirected graph from a pre-processing operation. The second step aims at determining a neighborhood for each sequence. The third step builds partial phylogenetic trees using results stemmed from step two. The steps are applied iteratively until the whole phylogenetic tree is obtained. A sequential code is available and it is currently implemented in parallel on a large cluster of PCs available at ID-IMAG.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>France</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Guinand, Frederic" sort="Guinand, Frederic" uniqKey="Guinand F" first="Frédéric" last="Guinand">Frédéric Guinand</name></noRegion></country><country name="France"><noRegion><name sortKey="Guinand, Frederic" sort="Guinand, Frederic" uniqKey="Guinand F" first="Frédéric" last="Guinand">Frédéric Guinand</name></noRegion><name sortKey="Parmentier, Gilles" sort="Parmentier, Gilles" uniqKey="Parmentier G" first="Gilles" last="Parmentier">Gilles Parmentier</name><name sortKey="Parmentier, Gilles" sort="Parmentier, Gilles" uniqKey="Parmentier G" first="Gilles" last="Parmentier">Gilles Parmentier</name><name sortKey="Trystram, Denis" sort="Trystram, Denis" uniqKey="Trystram D" first="Denis" last="Trystram">Denis Trystram</name><name sortKey="Trystram, Denis" sort="Trystram, Denis" uniqKey="Trystram D" first="Denis" last="Trystram">Denis Trystram</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/France/explor/LeHavreV1/Data/France/Analysis
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000F11 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/France/Analysis/biblio.hfd -nk 000F11 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/France
|area= LeHavreV1
|flux= France
|étape= Analysis
|type= RBID
|clé= ISTEX:52262FCF32545C90BD62024AB5E06B622D4A16A2
|texte= Construction of Phylogenetic Trees on Parallel Clusters
}}
| This area was generated with Dilib version V0.6.25. |  |