Your message dated Mon, 26 Mar 2007 10:14:24 +0200 (CEST) with message-id <Pine.LNX.4.62.0703261011190.23136@wr-linux02> and subject line Done: Bug#415418: components of phylip give wrong tree files has caused the attached Bug report to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what I am talking about this indicates a serious mail system misconfiguration somewhere. Please contact me immediately.) Debian bug tracking system administrator (administrator, Debian Bugs database)
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- To: submit@bugs.debian.org
- Subject: components of phylip give wrong tree files
- From: Elo Peter <elo@linux.vmri.hu>
- Date: Mon, 19 Mar 2007 13:40:40 +0100
- Message-id: <20070319124040.GA22635@linux.vmri.hu>
Package: phylip Version: 3.6.1-2 iDear maintainer, Various programs in the phylip package (proml, fitch) describe wrong phylogenetic trees. The problem should be in the common parts which outputs the "outtree" files. Since for example the distance matrix file produced by protdist is correct, but fitch -using this orrect matrix - describes the same nonsense tree like proml from the same alignment. Yours sincerely Peter Elo
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--- Begin Message ---
- To: 415418-done@bugs.debian.org
- Cc: Peter Elo <elo@linux.vmri.hu>
- Subject: Done: Bug#415418: components of phylip give wrong tree files
- From: Andreas Tille <tillea@rki.de>
- Date: Mon, 26 Mar 2007 10:14:24 +0200 (CEST)
- Message-id: <Pine.LNX.4.62.0703261011190.23136@wr-linux02>
- In-reply-to: <20070321133049.GA22828@gs.washington.edu>
- References: <Pine.LNX.4.62.0703201538220.14010@wr-linux02> <20070321133049.GA22828@gs.washington.edu>
On Wed, 21 Mar 2007, Joe Felsenstein wrote:5 18 p32kb4/94- ASRQFFNYRR PPDGEEDVDY QAKNKWSLED VISYLQHIPK QVRKVILTSL p32_rus/85 AARQYFNYRR PPDGEEDVDY NAKSKWNLED VISYLQHIPK QVRKVILTSL OAV_p32/10 ARDQWYFPIR PSDGEHDTDV KVKKKWSLDT VLQFLQSSPK HIRQLLLTSL EDS_p24k/1 APLYEEPIVK RSDGEADQDR AIKHKWNIDD VLDFLMKVPE RTRKVVLISL snake_p32k VAEGNYLPRR PADGEADRDN RVRNRWSLEQ VLRTLERIPA RGRKLILTGL FGATLGLIID ALLGGPWGLT TRLLRLIVSL VPGGKILLLA LDGLGYFLGK FGATLGLIID ALLGGPWGLT TRLLRLIVSL VPGGKILLLA LDGLGYFLGK FGSLLGLILD TLFGGPWNLT SRLLRLIISV VPGGRILLTA LDGLGYFLGN FGTAVGAVID LMLGSPLGLT SKIIRAILRI IPGGWIILNT FDGLGYLLGK FGTAVGVVLD LLLGSPLNLT TRLVRLIVGF VPGGNLILNA LDGLGYLMSR -NNNPNLVAY DPDLIKFGTN IQRNINGRLT EDIVRAAEEQ LGGGFMRTLA -SNNPNLVAY DPDLIKFGTD IQKNINGRLT EDIVRAAEEQ LGGGFMRTLA -SANPIHLIE NPMMQAFGNS IQKQISPRLA EDIIKAADEQ IGGGFMRTIA -GQEVLQITY DPGFVELAKR VQSSIPPHTA EEIAAAADRQ LGGNTFTASL FPSNPLQITY DPGFQRLANS VQQNIPQGTA EALAHAAEQQ VGEGFARNLA ALLSAAASAG THLKIALPAI PLAVIKPFQR ALLSAAASAG THLKIALPAI PLAVIKPFQR SILSAAASAG THFTMALPAI PIAAVRPFMR AALLHAVFLR D--R------ ---------- AAMSYLVGSA P--SAAPMAI PLALVRPFRP(p32_rus/85:0.02613,((snake_p32k:0.32827,EDS_p24k/1:0.70718):0.34711, OAV_p32/10:0.33825):0.24907,p32kb4/94-:0.02121);Looking at this "wierd" "wrong" "nonsense tree" it looks fine to me. Fitch and Proml output unrooted trees. The program defaults to rooting these on sequence number 1. That does not change the topology or branch lengths of the unrooted tree but can result in a startling tree if one thinks of it a rooted tree. If Peter were to choose a more reasonable outgroup, or else just look only at the unrooted shape of the tree, would he find anything wrong with it? One way to root the tree is to use the M (Midpoint rooting) option of Retree. If he still finds a problem I can chase it, but at this stage I don't think there is any.If upstream says this is the intended behaviour I do not see a reason to keep this bug open. There was no further response from the original bug reporter and thus either he is convinced and agrees with upstream or he should reopen the bug with further information what he would like upstream to change. Kind regards Andreas. -- http://fam-tille.de
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