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From: Sebastien M. <seb...@un...> - 2009-03-11 14:51:15
|
Hi, It seems that TreeFam API fails to return some genes for this family: TF105900. Both from the web site and in command line, the API returns 58 protein sequences for the 'clean' protein alignment, 58 external branches for the 'clean' tree BUT 56 nucleotides sequences for the 'clean' nucleotide alignment. BGIOSIFCE019517.1_ORYSA & BGIBMGA012703_BOMMO are not in the 'clean' nucleotide alignment. Do you have an idea why it happens ? Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ |
From: Sebastien M. <seb...@un...> - 2009-02-16 13:48:25
|
Hello, when do you plan to release MySQL dumps, and other data, from TreeFam 7 ? FTP data and links from www.treefam.org are always TreeFam 6 related. Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
From: Sebastien M. <seb...@un...> - 2009-02-09 08:17:59
|
Hello, when do you plan to release TreeFam 7 ? A TreeFam_7 database is now available on TreeFAM MySQL. Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ |
From: Jean-Karim H. <jk...@sa...> - 2008-10-22 07:22:34
|
Hi Sebastien, The current behaviour is to die on bad trees. I think this is the safest procedure as not doing so would allow further processing of bad trees. This would generate errors difficult to trace both in other parts of the API and in any code using the API. However, the error message could be more explicit and report on the family AC and type of tree causing the error. Would you also have the message say 'bad tree' instead of 'unrecognized format' ? J-K On Tue, 2008-10-21 at 12:15 +0200, Sebastien MORETTI wrote: > Hi, > > the API should return the same thing than the web site for 'Bad Tree' > like TF352160. > > It should be clearer for users. > > What do you think about it ? > |
From: Sebastien M. <seb...@un...> - 2008-10-21 10:15:37
|
Hi, the API should return the same thing than the web site for 'Bad Tree' like TF352160. It should be clearer for users. What do you think about it ? -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ |
From: Sebastien M. <Seb...@un...> - 2008-09-25 13:20:58
|
Hi Following 'Instructions' link on family pages I thought that Clean trees are clean because they use only sequences from sequenced species. And they are not manually curated compared to seed trees. Most of the time clean trees are larger than seed trees (e.g. TF101001). In some cases, e.g. TF106228, clean trees are smaller than seed trees. Although only sequenced species are available in the seed tree AND in the clean tree. So, what are the real differences between Clean, Seed and Full trees in TreeFam ? Only Clean trees in TreeFam B ? What should be the best kind of tree for large scale phylogenetic studies ? Thanks -- Sébastien Moretti |
From: Jean-Karim H. <jk...@sa...> - 2008-09-05 12:16:03
|
Hi Sebastien, Is the API not working because of this ? I believe that the API produces a correct tree and that the database is possibly wrong: the database tree should have an empty [&&NHX] (this was the case in previous versions of Treefam). Having [&&NHX] makes the nodes consistent and I think this doesn't violate the specifications of the format. This is down to the interpretation of the format: Should a node with no information get an empty [&&NHX] or nothing ? What do other treefamers think ? J-K On Fri, 2008-09-05 at 11:18 +0200, Sebastien Moretti wrote: > Hi, > It seems that API produces an invalid HNX tree for TF102048 family. > > From the database (TreeFam6), the tree looks proper. > Here is a view: > ... > T=8090:G=ENSORLG00000004203]):1.7):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX > ... > > There is no NHX information for the 1.7 branch long. > Nevertheless, the API returns this: > ... > T=8090:G=ENSORLG00000004203]):1.7[&&NHX]):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX > ... > > > 1.7[&&NHX] instead of 1.7 > > How to fix this ? > Thanks > |
From: Sebastien M. <Seb...@un...> - 2008-09-05 09:18:58
|
Hi, It seems that API produces an invalid HNX tree for TF102048 family. From the database (TreeFam6), the tree looks proper. Here is a view: ... T=8090:G=ENSORLG00000004203]):1.7):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX ... There is no NHX information for the 1.7 branch long. Nevertheless, the API returns this: ... T=8090:G=ENSORLG00000004203]):1.7[&&NHX]):0.070715[&&NHX:S=Percomorpha:D=N:B=23]):0.104119[&&NHX ... 1.7[&&NHX] instead of 1.7 How to fix this ? Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
From: Sebastien M. <Seb...@un...> - 2008-08-25 13:05:56
|
Here is a list of duplicated entries I found. All of them seem to come from Schistosoma mansoni species. Smp_150040.1 Smp_062300 Smp_028100.1 Smp_059750 Smp_136850.1 Smp_165350.1 Smp_138920.1 Smp_176260.1 Smp_159900.1 Smp_074070.1 Smp_061920.1 Smp_093750.1 Smp_103460.1 Smp_060940 Smp_176230.1 Smp_041430.1 Smp_034840.1 Smp_034840.1 Smp_153760.1 Smp_055760 Smp_094050.1 Smp_009650.1 Smp_069130.1 Smp_106130.1 Smp_049300.1 Smp_049300.1 Smp_049300.1 Smp_144010.1 Smp_162800.1 Smp_059290.1 Smp_176200.1 Smp_163420.1 Smp_020920.1 Smp_035200.1 Smp_035200.1 Smp_035200.1 Smp_049600.1 Smp_049600.1 Smp_049600.1 Smp_005070.1 Smp_138680.1 Smp_158110.1 Smp_004470.1 Smp_004470.1 Smp_035720 Smp_147250.1 Smp_128200.1 Smp_149200.1 Smp_149200.1 Smp_076030.1 Smp_033050.1 Smp_033050.1 Smp_004780.1 Smp_158320.1 Smp_064040 Smp_161970.1 Smp_104680.1 Smp_034980.1 Smp_035430.1 Smp_025570.1 Smp_025570.1 Smp_042590.1 Smp_063120.1 Smp_063120.1 Smp_160770.1 Smp_160770.1 Smp_045430.1 Smp_054790.1 Smp_054340.1 Smp_054340.1 Smp_042270.1 Smp_042270.1 Smp_038080.1 Smp_005080.1 Smp_005080.1 Smp_066630.1 Smp_046880.1 Smp_053510.1 Smp_173180.1 Smp_141630.1 Smp_141630.1 Smp_141630.1 Smp_124820.1 Smp_046090.1 Smp_096450 Smp_120320 Smp_075220.1 Smp_075220.1 Smp_000030.1 Smp_000030.1 Smp_076630.1 Smp_030930.1 Smp_142010.1 Smp_038870.1 Smp_050360 Smp_033670.1 Smp_033670.1 Smp_033670.1 Smp_058150.1 Smp_031040 Smp_024060.1 Smp_001410 Smp_031950.1 Smp_009420 Smp_103930.1 Smp_103930.1 Smp_103930.1 Smp_103930.1 Smp_035270.1 Smp_048260.1 Smp_130790.1 Smp_042670.1 Smp_031000.1 Smp_138970.1 Smp_042430.1 Smp_064020.2 Smp_064020.2 Smp_064020.2 Smp_079050.1 Smp_069220 Smp_055420.1 Smp_007630.1 Smp_063580.1 Smp_063580.1 Smp_156440.2 Smp_096780.1 Smp_106080.1 Smp_066960.1 Smp_082560.1 Smp_175120.1 Smp_085310.1 Smp_045750 Smp_140450.1 Smp_010230 Smp_061310.1 Smp_061310.1 Smp_084140.1 Smp_084140.1 Smp_095910.1 Smp_017290.3 Smp_165810.2 Smp_024360 Smp_030920.1 Smp_032580.1 Smp_032580.1 Smp_121430.1 Smp_074500 Smp_000740.1 Smp_066340 Smp_048280.1 Smp_098890.1 Smp_098890.1 Smp_045950.1 Smp_079430.1 Smp_052280.1 Smp_065190 Smp_165140.1 Smp_150850.1 Smp_121610.1 Smp_121610.1 Smp_128890.1 Smp_014400.1 Smp_014400.1 Smp_014400.1 Smp_049730 Smp_168850.1 Smp_101370 Smp_006250.1 Smp_053220.1 Cheers Sébastien > Maybe the best way will be to remove redundancy into the gene list (from > leaves) because I get 2 Smp_150040 entries. > > Then extract alignment(s) for every geneID. > > > What do you think about ? > > Cheers > Sébastien > >>> Hi Sebastien, >>> >>> The example you give looks strange because a gene should only be >>> represented by >>> one transcript in a given tree. >> I think I can find several other examples like this one. >> >>> Anyone got an idea why a gene can be represented by 2 transcripts in the >>> same >>> tree ? >> It seems these transcripts are too distant and that they cannot be >> merged as one single gene. >> >>> I'll see how to fix the API for cases like this. >> > >>> Cheers >>> >>> J-K >> Thanks >> Sébastien >> >>> Quoting Sebastien MORETTI <Seb...@un...>: >>> >>>> Hi, >>>> >>>> we use your API which is very powerful. >>>> But there is a problem when we try to get the alignment for families = >>>> >>>> where one GID (GeneID) is the same for 2 or more leaves: >>>> e.g. 1 Family TF101024 >>>> 1 GID Smp_150040 >>>> 2 leaves Smp_150040.1 & Smp_150040.2 >>>> >>>> the nhx method returns the proper tree with distinct Smp_150040.1 & = >>>> >>>> Smp_150040.2 >>>> But the get_alignment method returns twice Smp_150040.1, with the same = >>>> >>>> headers and sequences. Smp_150040.1 is duplicated. >>>> >>>> >>>> How to resolve this ? >>>> >>>> Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 |
From: Sebastien M. <Seb...@un...> - 2008-08-25 12:57:14
|
Maybe the best way will be to remove redundancy into the gene list (from leaves) because I get 2 Smp_150040 entries. Then extract alignment(s) for every geneID. What do you think about ? Cheers Sébastien >> Hi Sebastien, >> >> The example you give looks strange because a gene should only be >> represented by >> one transcript in a given tree. > > I think I can find several other examples like this one. > >> Anyone got an idea why a gene can be represented by 2 transcripts in the >> same >> tree ? > > It seems these transcripts are too distant and that they cannot be > merged as one single gene. > >> I'll see how to fix the API for cases like this. > > >> Cheers >> >> J-K > > Thanks > Sébastien > >> Quoting Sebastien MORETTI <Seb...@un...>: >> >>> Hi, >>> >>> we use your API which is very powerful. >>> But there is a problem when we try to get the alignment for families = >>> >>> where one GID (GeneID) is the same for 2 or more leaves: >>> e.g. 1 Family TF101024 >>> 1 GID Smp_150040 >>> 2 leaves Smp_150040.1 & Smp_150040.2 >>> >>> the nhx method returns the proper tree with distinct Smp_150040.1 & = >>> >>> Smp_150040.2 >>> But the get_alignment method returns twice Smp_150040.1, with the same = >>> >>> headers and sequences. Smp_150040.1 is duplicated. >>> >>> >>> How to resolve this ? >>> >>> Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 |
From: Sebastien M. <Seb...@un...> - 2008-08-25 12:49:31
|
> Hi Sebastien, > > The example you give looks strange because a gene should only be > represented by > one transcript in a given tree. I think I can find several other examples like this one. > Anyone got an idea why a gene can be represented by 2 transcripts in the > same > tree ? It seems these transcripts are too distant and that they cannot be merged as one single gene. > I'll see how to fix the API for cases like this. > > Cheers > > J-K Thanks Sébastien > Quoting Sebastien MORETTI <Seb...@un...>: > >> Hi, >> >> we use your API which is very powerful. >> But there is a problem when we try to get the alignment for families = >> >> where one GID (GeneID) is the same for 2 or more leaves: >> e.g. 1 Family TF101024 >> 1 GID Smp_150040 >> 2 leaves Smp_150040.1 & Smp_150040.2 >> >> the nhx method returns the proper tree with distinct Smp_150040.1 & = >> >> Smp_150040.2 >> But the get_alignment method returns twice Smp_150040.1, with the same = >> >> headers and sequences. Smp_150040.1 is duplicated. >> >> >> How to resolve this ? >> >> Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 |
From: Sebastien M. <Seb...@un...> - 2008-08-25 12:22:43
|
Hi, we use your API which is very powerful. But there is a problem when we try to get the alignment for families where one GID (GeneID) is the same for 2 or more leaves: e.g. 1 Family TF101024 1 GID Smp_150040 2 leaves Smp_150040.1 & Smp_150040.2 the nhx method returns the proper tree with distinct Smp_150040.1 & Smp_150040.2 But the get_alignment method returns twice Smp_150040.1, with the same headers and sequences. Smp_150040.1 is duplicated. How to resolve this ? Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 |
From: Sebastien M. <Seb...@un...> - 2008-06-24 07:40:45
|
Hi, It seems that MySQL dumps for TreeFam 6.0 are not the good one. When I connect to TreeFam.org (mysql -u anonymous -h db.treefam.org -P3308 treefam_6) I get 50 species with this request: SELECT * FROM species WHERE FLAG=1; With the dump from ftp://ftp.sanger.ac.uk/pub/treefam/release-6.0/MySQL/ or ftp://ftp.sanger.ac.uk/pub/treefam/release-current/MySQL/ locally, I get only 29 species with the same request. It is the same number than in TreeFam 4.0 or 5.0 . Do I do something wrong ? Or only the species table is fake ? Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ |
From: Sebastien M. <Seb...@un...> - 2008-05-13 14:31:01
|
Hi, We are trying to install and use TreeFam locally. Everything is fine on database side but we encounter some problems with the APIs. First, when we try to use e.g. tfscripts/cgi-bin/search2.pl, a Perl module is missing (SangerWeb.pm) and not provided from the SVN. Is this module mandatory ? Where can we get it ? Second, the SVN repository does not seem to provide the configuration file required to run tfscripts/treefam.pl Third, when we try to use tfscripts/cgi-bin/treeview.pl a Perl module is missing (private.pm) and not provided from the SVN in the developer-oriented perl APIs. Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 |
From: Lukasz H. <Luk...@ki...> - 2008-04-30 18:08:22
|
Dear Treefam, First of all, I must say "thank you" for an incredible resource! The quality of trees is astonishing. So much so, that I installed TreeBest locally and I am trying to use it with mixture of my own sequences plus sequences for my family derived from the MySQL version of Treefam5, which I also downloaded from your website. However, as Treefam5 has many more species than Treefam4, I badly need a new species tree for use with TreeBest. Could you help, please? I tried using the binary tree_of_life_1.4 which comes with the ATV viewer, but TreeBest does not seem to like the format of this tree. Or maybe there is a way ti build TreeBest compatible species treees directly from NCBI's taxonomy resources (I have a few species in addition to Treefam5 species)? all the best, Lukasz |
From: Sebastien M. <Seb...@un...> - 2008-03-18 10:27:25
|
> Hi, >> Is there a simple way to get TreeFam current release ? >> >> Via database request or treesoft API ? > > You should be able to access all Treefam versions on the MySQL server. > We are currently working on version 6. However, the only stable version > is the public one (currently version 4). The API goes with the public > version. We made some modifications in Treefam 6 so the current public > API (v4) may not work for everything. > > J-K So, if treesoft API is always up-to-date locally, we are able to know the current TreeFam release simply with the $Treefam::Config::APIVERSION or $Treefam::Config::TFDBNAME variables. Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 |
From: Sebastien M. <Seb...@un...> - 2008-03-18 10:05:00
|
Hi, Is there a simple way to get TreeFam current release ? Via database request or treesoft API ? Thanks -- Sébastien Moretti |
From: Heng Li <lh...@sa...> - 2006-11-22 11:29:07
|
Hello Helder Ribeiro, Really thank you for your interest in NJTREE. I am sorry that I do not know whether there is free softwares that can implements parsimony jackknifing, and I am afraid that myself may not have enough time to study and implement this in the near future. We are busy with the upcoming TreeFam-4. However, we are really interested in Parsimony Jackknifing, and we want to make NJTREE more powerful. If you are to implement, we will be willing to incorporate your codes to NJTREE. You are more than welcomed. We may establish further contact if you'd like to. Cheers, Heng ------------------------------ >Hello, > > I only recently came across NJTREE through SourceForge while I was > looking for a program that implemented Parsimony Jackknifing. I > haven't found any yet (except for the proprietary PAUP with its > many-thousand-dollar license). > > I would like to know if anyone knows of any free software which > implements PJ or some other kind of tree-building-with-resampling > technique (like bootstrapping). If there is none, would this be > something interesting for the future of NJTREE? If I were to implement > if myself, would it be ok to have it done as a new feature for NJTREE? > > Great work, by the way. =) > > Cheers, > > Helder Ribeiro > > Institute of Computing > State University of Campinas > Campinas - SP > Brazil |
From: Helder R. <he...@gm...> - 2006-11-21 02:53:18
|
Hello, I only recently came across NJTREE through SourceForge while I was looking for a program that implemented Parsimony Jackknifing. I haven't found any yet (except for the proprietary PAUP with its many-thousand-dollar license). I would like to know if anyone knows of any free software which implements PJ or some other kind of tree-building-with-resampling technique (like bootstrapping). If there is none, would this be something interesting for the future of NJTREE? If I were to implement if myself, would it be ok to have it done as a new feature for NJTREE? Great work, by the way. =) Cheers, Helder Ribeiro Institute of Computing State University of Campinas Campinas - SP Brazil |