GSF - The Genetic Software Forum
Questions and answers about the use of software for genetic analysis
PAML
Moderator: Ziheng
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- Please use the UCL site to post questions about PAML
by Ziheng » Mon Feb 02, 2009 3:11 pm - 0 Replies
- 249 Views
- Last post by Ziheng
Mon Feb 02, 2009 3:11 pm
- Please use the UCL site to post questions about PAML
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- a new paml discussion site
by Ziheng » Sat Dec 06, 2008 2:02 am - 1 Replies
- 458 Views
- Last post by brannala
Wed Feb 04, 2009 1:59 am
- a new paml discussion site
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- Topics
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- local clock : need fossils for this locus
by blue esprit » Sat Sep 27, 2008 5:25 am - 1 Replies
- 450 Views
- Last post by Ziheng
Tue Feb 24, 2009 10:05 pm
- local clock : need fossils for this locus
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- no standard error with free branch model and fixed branches
by Danny » Mon Nov 10, 2008 8:15 pm - 2 Replies
- 146 Views
- Last post by Ziheng
Mon Feb 02, 2009 3:06 pm
- no standard error with free branch model and fixed branches
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- no ancestral sequence in rst file (codeml)
by zevkronenberg » Mon Nov 17, 2008 10:26 pm - 3 Replies
- 190 Views
- Last post by Ziheng
Mon Feb 02, 2009 3:01 pm
- no ancestral sequence in rst file (codeml)
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- who can help me lable a tree use 4 ratio model
by liwenle » Wed Dec 17, 2008 11:33 am - 1 Replies
- 132 Views
- Last post by Ziheng
Mon Feb 02, 2009 2:49 pm
- who can help me lable a tree use 4 ratio model
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- How to get site-specific dS values?
by Kreitenga » Mon Dec 22, 2008 4:43 pm - 1 Replies
- 111 Views
- Last post by Ziheng
Mon Feb 02, 2009 2:33 pm
- How to get site-specific dS values?
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- HYPHY for detecting positive selection
by genejockey » Tue Jan 06, 2009 8:14 pm - 1 Replies
- 135 Views
- Last post by Ziheng
Mon Feb 02, 2009 2:15 pm
- HYPHY for detecting positive selection
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- Correction for Branch-site model
by raisnow » Tue Dec 02, 2008 4:00 am - 3 Replies
- 306 Views
- Last post by Ziheng
Mon Feb 02, 2009 2:08 pm
- Correction for Branch-site model
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- Sequence length affecting global dN/dS?
by Hiacynt » Mon Jan 12, 2009 3:13 pm - 1 Replies
- 103 Views
- Last post by Ziheng
Mon Feb 02, 2009 1:52 pm
- Sequence length affecting global dN/dS?
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- rounding error
by katanu » Mon Jan 12, 2009 10:03 pm - 1 Replies
- 63 Views
- Last post by Ziheng
Mon Feb 02, 2009 1:40 pm
- rounding error
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- no result by yn00
by haili » Tue Nov 18, 2008 5:21 pm - 1 Replies
- 93 Views
- Last post by Ziheng
Mon Feb 02, 2009 1:36 pm
- no result by yn00
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- branch model
by liwenle » Wed Dec 17, 2008 6:15 am - 1 Replies
- 116 Views
- Last post by Ziheng
Mon Feb 02, 2009 1:34 pm
- branch model
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- labeling a tree
by zzxx » Wed Sep 24, 2008 6:17 pm - 2 Replies
- 269 Views
- Last post by Ziheng
Mon Feb 02, 2009 1:24 pm
- labeling a tree
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- Pamp error: 'err:PathwayMP'
by abhiman » Thu Apr 21, 2005 12:56 pm - 8 Replies
- 874 Views
- Last post by vg629911
Fri Jan 09, 2009 3:16 am
- Pamp error: 'err:PathwayMP'
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- bonferroni correction
by tamara » Sun Aug 27, 2006 9:08 am - 4 Replies
- 1060 Views
- Last post by vcgold
Thu Dec 25, 2008 6:31 am
- bonferroni correction
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- AAClasses for particular branches
by tbedford » Sun Apr 15, 2007 9:24 pm - 4 Replies
- 860 Views
- Last post by Ziheng
Sun Dec 21, 2008 11:29 am
- AAClasses for particular branches
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- dn/ds estimates and indels.
by stephane » Mon Dec 01, 2008 4:31 am - 2 Replies
- 292 Views
- Last post by stephane
Wed Dec 10, 2008 9:42 am
- dn/ds estimates and indels.
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- LRT for sites, significance and BEB
by lupeix » Mon Nov 17, 2008 4:35 pm - 1 Replies
- 149 Views
- Last post by Ziheng
Sat Dec 06, 2008 1:25 am
- LRT for sites, significance and BEB
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- Difference between clock2 and clock3
by beginbayes » Sun Nov 09, 2008 4:55 am - 1 Replies
- 179 Views
- Last post by Ziheng
Sat Dec 06, 2008 1:12 am
- Difference between clock2 and clock3
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- using dnds obtained from a concatenate
by maggie8 » Tue Nov 11, 2008 5:11 pm - 1 Replies
- 100 Views
- Last post by Ziheng
Sat Dec 06, 2008 12:32 am
- using dnds obtained from a concatenate
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- no result by yn00
by haili » Tue Nov 18, 2008 5:14 pm - 1 Replies
- 109 Views
- Last post by Ziheng
Sat Dec 06, 2008 12:28 am
- no result by yn00
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- unusual high numbers in the modelinf.-file
by Axel » Mon Nov 24, 2008 7:07 pm - 0 Replies
- 66 Views
- Last post by Axel
Mon Nov 24, 2008 7:07 pm
- unusual high numbers in the modelinf.-file
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- adaptation by pseudogenization
by Petr » Mon Sep 15, 2008 11:00 am - 5 Replies
- 389 Views
- Last post by Petr
Thu Nov 13, 2008 2:34 pm
- adaptation by pseudogenization
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- Problems on installing PAML 4.1?
by Wen » Thu Sep 18, 2008 8:49 pm - 4 Replies
- 365 Views
- Last post by davidm
Mon Nov 10, 2008 4:25 pm
- Problems on installing PAML 4.1?
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- A question about the YN00
by gohidg » Sat Nov 08, 2008 8:56 am - 1 Replies
- 142 Views
- Last post by Ziheng
Sat Nov 08, 2008 1:02 pm
- A question about the YN00
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- Branch site model A, ps only on 2b site class
by barnaba44 » Fri Oct 24, 2008 11:51 am - 1 Replies
- 208 Views
- Last post by Ziheng
Sat Nov 08, 2008 12:49 pm
- Branch site model A, ps only on 2b site class
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- d4 synonymous rate
by Ted Mes » Fri Dec 24, 2004 7:29 am - 13 Replies
- 2444 Views
- Last post by Ziheng
Sat Nov 08, 2008 12:34 pm
- d4 synonymous rate
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- LRTs for Models
by kopaka_nuva » Wed Oct 29, 2008 11:57 pm - 1 Replies
- 167 Views
- Last post by Ziheng
Sat Nov 08, 2008 12:16 pm
- LRTs for Models
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- handle heterozygotes in codeml
by cvillamar » Thu Oct 09, 2008 10:37 am - 1 Replies
- 150 Views
- Last post by Ziheng
Sat Nov 08, 2008 12:02 pm
- handle heterozygotes in codeml
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- N and S in codeml output
by ishengtsai » Mon Oct 20, 2008 9:47 am - 1 Replies
- 213 Views
- Last post by Ziheng
Sat Nov 08, 2008 11:52 am
- N and S in codeml output
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- error msg as species A?
by neha » Mon Sep 22, 2008 4:25 pm - 1 Replies
- 217 Views
- Last post by Ziheng
Sat Nov 08, 2008 11:41 am
- error msg as species A?
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- check convergence and rooted input tree
by fxb142 » Wed Oct 08, 2008 10:44 pm - 1 Replies
- 174 Views
- Last post by Ziheng
Mon Oct 27, 2008 10:20 pm
- check convergence and rooted input tree
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- How to interpret positive selection under two situations?
by allengalaxaura » Sat Jul 19, 2008 5:25 am - 4 Replies
- 517 Views
- Last post by Ziheng
Mon Oct 27, 2008 10:04 pm
- How to interpret positive selection under two situations?
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- check convergence and rooted input tree
by fxb142 » Wed Oct 08, 2008 10:58 pm - 0 Replies
- 131 Views
- Last post by fxb142
Wed Oct 08, 2008 10:58 pm
- check convergence and rooted input tree
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- understandig the result outfile of baseml
by sterding » Tue Sep 02, 2008 11:32 am - 1 Replies
- 245 Views
- Last post by Ziheng
Sat Sep 20, 2008 5:44 pm
- understandig the result outfile of baseml
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- codonml output for positive selection
by pzt » Fri Sep 05, 2008 9:56 pm - 1 Replies
- 326 Views
- Last post by Ziheng
Sat Sep 20, 2008 5:03 pm
- codonml output for positive selection
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- The smaller M8 lnL than null model, why?
by cryptocoryne » Tue Sep 02, 2008 4:02 am - 1 Replies
- 229 Views
- Last post by Ziheng
Sat Sep 20, 2008 4:50 pm
- The smaller M8 lnL than null model, why?
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- Dn/Ds greater than 1 but no PS?
by phylotree » Mon Sep 01, 2008 2:09 pm - 1 Replies
- 289 Views
- Last post by Ziheng
Sat Sep 20, 2008 4:44 pm
- Dn/Ds greater than 1 but no PS?
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- question about detecting extra purify selection pressure
by sterding » Wed Aug 27, 2008 2:29 pm - 1 Replies
- 275 Views
- Last post by Ziheng
Sun Aug 31, 2008 6:21 pm
- question about detecting extra purify selection pressure
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- multidiv time
by Miloje » Thu Aug 07, 2008 1:45 pm - 1 Replies
- 294 Views
- Last post by Ziheng
Tue Aug 26, 2008 5:25 pm
- multidiv time
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- in frame stop codon
by tan » Sat Aug 02, 2008 9:31 am - 3 Replies
- 368 Views
- Last post by Ziheng
Tue Aug 26, 2008 5:23 pm
- in frame stop codon
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- dN dS ratio
by deep1 » Thu Aug 07, 2008 10:20 pm - 1 Replies
- 364 Views
- Last post by Ziheng
Tue Aug 26, 2008 5:20 pm
- dN dS ratio
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- baseml for multidivtime analysis
by Leish » Fri Aug 08, 2008 2:34 am - 1 Replies
- 232 Views
- Last post by Ziheng
Tue Aug 26, 2008 5:17 pm
- baseml for multidivtime analysis
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- 2NG.dN and 2NG.dS were missed
by cuijack » Wed Aug 13, 2008 12:58 am - 1 Replies
- 224 Views
- Last post by Ziheng
Tue Aug 26, 2008 5:10 pm
- 2NG.dN and 2NG.dS were missed
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- Problem when using branch model
by cuijack » Wed Aug 13, 2008 8:20 am - 1 Replies
- 263 Views
- Last post by Ziheng
Tue Aug 26, 2008 5:02 pm
- Problem when using branch model
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- Where to get FMutSel and FMutSel0 models?
by Chris » Sat Aug 16, 2008 10:50 am - 1 Replies
- 255 Views
- Last post by Ziheng
Tue Aug 26, 2008 4:55 pm
- Where to get FMutSel and FMutSel0 models?
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- how to test if difference btw models is sig if d.f=0
by tania » Sat Aug 16, 2008 9:03 pm - 1 Replies
- 228 Views
- Last post by Ziheng
Tue Aug 26, 2008 4:50 pm
- how to test if difference btw models is sig if d.f=0
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- codeml output getting truncated
by munirul » Thu Aug 21, 2008 2:47 pm - 1 Replies
- 292 Views
- Last post by Ziheng
Tue Aug 26, 2008 4:45 pm
- codeml output getting truncated
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- variation in pairwise dS output
by derek_gatherer » Tue Aug 26, 2008 7:53 am - 1 Replies
- 171 Views
- Last post by Ziheng
Tue Aug 26, 2008 4:43 pm
- variation in pairwise dS output
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- divergence time estimation
by Miloje » Sat Aug 02, 2008 6:25 pm - 1 Replies
- 308 Views
- Last post by Ziheng
Tue Aug 26, 2008 4:33 pm
- divergence time estimation
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