Re: [Binari] Software.FastTree 2.0.0 for inferring large any experience?
Who the fuck? Joris Meys wrote:
Dear all,
I'm currently writing my master dissertation under the supervision of Jens. I read the announcement of FastTree 2 in the mail this week, and it would greatly help me, as I have to build a few thousand trees in a rather short time frame. I'm not afraid of figuring out how it works myself, but if anybody has some tips, they are greatly appreciated. Thank you in advance
Joris
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Subject: [Fwd: Other: Software.FastTree 2.0.0 for inferring large] From: Yves Van de Peer <yves.vandepeer@psb.vib-ugent.be> Date: Sat, 01 Aug 2009 08:52:31 +0200 To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be>
To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be>
-------- Original Message -------- Subject: Other: Software.FastTree 2.0.0 for inferring large Date: Sat, 1 Aug 2009 02:40:28 -0400 (EDT) From: evoldir@evol.biology.mcmaster.ca Reply-To: brian@helix.biology.mcmaster.ca To: yves.vandepeer@psb.ugent.be
We announce FastTree 2, a tool for inferring approximately maximum-likelihood trees for large alignments. FastTree is more accurate than PhyML 3's default settings and 100-1,000 times faster than PhyML or RAxML. FastTree analyzed an alignment of >200,000 16S ribosomal RNAs in a day on a desktop computer.
Models: Jukes-Cantor or GTR (nucleotide) or JTT (amino acid) Rate variation across sites: the CAT approximation (1 rate per site) Support values: local SH-like supports (or global bootstrap)
FastTree 2 is available at http://www.microbesonline.org/fasttree/
Morgan N. Price & Paramvir S. Dehal Physical Biosciences Division Lawrence Berkeley National Lab fasttree@microbesonline.org
morgannprice@yahoo.com
-- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be
The guy sitting next to Jens I guess? It's weird how Jens has his own world .. euhm .. group somehow. He totally skips lunchmeeting presentations and indeed .. fails to introduce new people. ;) Kenny On Fri, 7 Aug 2009, Sofie Van Landeghem wrote:
Who the fuck?
Joris Meys wrote:
Dear all,
I'm currently writing my master dissertation under the supervision of Jens. I read the announcement of FastTree 2 in the mail this week, and it would greatly help me, as I have to build a few thousand trees in a rather short time frame. I'm not afraid of figuring out how it works myself, but if anybody has some tips, they are greatly appreciated. Thank you in advance
Joris
------------------------------------------------------------------------
Subject: [Fwd: Other: Software.FastTree 2.0.0 for inferring large] From: Yves Van de Peer <yves.vandepeer@psb.vib-ugent.be> Date: Sat, 01 Aug 2009 08:52:31 +0200 To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be>
To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be>
-------- Original Message -------- Subject: Other: Software.FastTree 2.0.0 for inferring large Date: Sat, 1 Aug 2009 02:40:28 -0400 (EDT) From: evoldir@evol.biology.mcmaster.ca Reply-To: brian@helix.biology.mcmaster.ca To: yves.vandepeer@psb.ugent.be
We announce FastTree 2, a tool for inferring approximately maximum-likelihood trees for large alignments. FastTree is more accurate than PhyML 3's default settings and 100-1,000 times faster than PhyML or RAxML. FastTree analyzed an alignment of >200,000 16S ribosomal RNAs in a day on a desktop computer.
Models: Jukes-Cantor or GTR (nucleotide) or JTT (amino acid) Rate variation across sites: the CAT approximation (1 rate per site) Support values: local SH-like supports (or global bootstrap)
FastTree 2 is available at http://www.microbesonline.org/fasttree/
Morgan N. Price & Paramvir S. Dehal Physical Biosciences Division Lawrence Berkeley National Lab fasttree@microbesonline.org
morgannprice@yahoo.com
-- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau@ugent.be http://bioinformatics.psb.ugent.be ================================================================== "What we feel isn't important. The only question is what we do." -- Rohl
Are we sure Jens never introduced Joris in one of the newsletters? If not, maybe Sofie or Kenny (as editors) can ask him to do so next time, with a reference to the mail of Joris today or something? Tine °°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°° Tine Blomme Bioinformatics group VIB department of Plant Systems Biology Ghent University Technologiepark 927, B-9052 Zwijnaarde Tel: +32 (0)9 331 38 22 Op 7-aug-09, om 13:42 heeft Kenny Billiau het volgende geschreven:
The guy sitting next to Jens I guess?
It's weird how Jens has his own world .. euhm .. group somehow. He totally skips lunchmeeting presentations and indeed .. fails to introduce new people. ;)
Kenny
On Fri, 7 Aug 2009, Sofie Van Landeghem wrote:
Who the fuck?
Joris Meys wrote:
Dear all,
I'm currently writing my master dissertation under the supervision of Jens. I read the announcement of FastTree 2 in the mail this week, and it would greatly help me, as I have to build a few thousand trees in a rather short time frame. I'm not afraid of figuring out how it works myself, but if anybody has some tips, they are greatly appreciated. Thank you in advance
Joris
------------------------------------------------------------------------
Subject: [Fwd: Other: Software.FastTree 2.0.0 for inferring large] From: Yves Van de Peer <yves.vandepeer@psb.vib-ugent.be> Date: Sat, 01 Aug 2009 08:52:31 +0200 To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be>
To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be>
-------- Original Message -------- Subject: Other: Software.FastTree 2.0.0 for inferring large Date: Sat, 1 Aug 2009 02:40:28 -0400 (EDT) From: evoldir@evol.biology.mcmaster.ca Reply-To: brian@helix.biology.mcmaster.ca To: yves.vandepeer@psb.ugent.be
We announce FastTree 2, a tool for inferring approximately maximum-likelihood trees for large alignments. FastTree is more accurate than PhyML 3's default settings and 100-1,000 times faster than PhyML or RAxML. FastTree analyzed an alignment of >200,000 16S ribosomal RNAs in a day on a desktop computer.
Models: Jukes-Cantor or GTR (nucleotide) or JTT (amino acid) Rate variation across sites: the CAT approximation (1 rate per site) Support values: local SH-like supports (or global bootstrap)
FastTree 2 is available at http://www.microbesonline.org/fasttree/
Morgan N. Price & Paramvir S. Dehal Physical Biosciences Division Lawrence Berkeley National Lab fasttree@microbesonline.org
morgannprice@yahoo.com
-- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau@ugent.be http://bioinformatics.psb.ugent.be ================================================================== "What we feel isn't important. The only question is what we do." -- Rohl _______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
We have a face, people! Start preparing the wall of shame, he's on the cluster as we speak. Tine Blomme wrote:
Are we sure Jens never introduced Joris in one of the newsletters? If not, maybe Sofie or Kenny (as editors) can ask him to do so next time, with a reference to the mail of Joris today or something?
Tine
°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°° Tine Blomme
Bioinformatics group VIB department of Plant Systems Biology Ghent University
Technologiepark 927, B-9052 Zwijnaarde
Tel: +32 (0)9 331 38 22
Op 7-aug-09, om 13:42 heeft Kenny Billiau het volgende geschreven:
The guy sitting next to Jens I guess?
It's weird how Jens has his own world .. euhm .. group somehow. He totally skips lunchmeeting presentations and indeed .. fails to introduce new people. ;)
Kenny
On Fri, 7 Aug 2009, Sofie Van Landeghem wrote:
Who the fuck?
Joris Meys wrote:
Dear all,
I'm currently writing my master dissertation under the supervision of Jens. I read the announcement of FastTree 2 in the mail this week, and it would greatly help me, as I have to build a few thousand trees in a rather short time frame. I'm not afraid of figuring out how it works myself, but if anybody has some tips, they are greatly appreciated. Thank you in advance
Joris
------------------------------------------------------------------------
Subject: [Fwd: Other: Software.FastTree 2.0.0 for inferring large] From: Yves Van de Peer <yves.vandepeer@psb.vib-ugent.be <mailto:yves.vandepeer@psb.vib-ugent.be>> Date: Sat, 01 Aug 2009 08:52:31 +0200 To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be <mailto:beg@psb.ugent.be>>
To: Bioinformatics & Evolutionary Genomics <beg@psb.ugent.be <mailto:beg@psb.ugent.be>>
-------- Original Message -------- Subject: Other: Software.FastTree 2.0.0 for inferring large Date: Sat, 1 Aug 2009 02:40:28 -0400 (EDT) From: evoldir@evol.biology.mcmaster.ca <mailto:evoldir@evol.biology.mcmaster.ca> Reply-To: brian@helix.biology.mcmaster.ca <mailto:brian@helix.biology.mcmaster.ca> To: yves.vandepeer@psb.ugent.be <mailto:yves.vandepeer@psb.ugent.be>
We announce FastTree 2, a tool for inferring approximately maximum-likelihood trees for large alignments. FastTree is more accurate than PhyML 3's default settings and 100-1,000 times faster than PhyML or RAxML. FastTree analyzed an alignment of >200,000 16S ribosomal RNAs in a day on a desktop computer.
Models: Jukes-Cantor or GTR (nucleotide) or JTT (amino acid) Rate variation across sites: the CAT approximation (1 rate per site) Support values: local SH-like supports (or global bootstrap)
FastTree 2 is available at http://www.microbesonline.org/fasttree/
Morgan N. Price & Paramvir S. Dehal Physical Biosciences Division Lawrence Berkeley National Lab fasttree@microbesonline.org <mailto:fasttree@microbesonline.org>
morgannprice@yahoo.com <mailto:morgannprice@yahoo.com>
-- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau@ugent.be http://bioinformatics.psb.ugent.be ================================================================== "What we feel isn't important. The only question is what we do." -- Rohl _______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
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_______________________________________________ Binari Implicitly Neglects All Recursive Iterations https://maillist.psb.ugent.be/mailman/listinfo/binari
-- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be
participants (4)
-
Joost Van Den Cruyce -
Kenny Billiau -
Sofie Van Landeghem -
Tine Blomme