Hi Joe,
I just want you make aware of a bug that was reported to the Debian
bug tracking system.
http://bugs.debian.org/415418
Below you can find some more information and attached are the
data files. Would you be able to verify this? It is a problem
in Phylip itself or just the Debian packaged version?
Kind regards and thanks for providing Phylip
Andreas.
--
http://fam-tille.de
---------- Forwarded message ----------
Date: Mon, 19 Mar 2007 14:51:13 +0100
From: Elo Peter <[EMAIL PROTECTED]>
To: Andreas Tille <[EMAIL PROTECTED]>
Subject: Re: Bug#415418: components of phylip give wrong tree files
Thanks for the bug report. I have to admit that I do not use phylip
personally and thus I have to relay on a very detailed description
of your problem. At first I would like you to ask whether you could
upgrade aour phalip version currently residing in unstable. It is
not that the package of phylip itself is unstable but it will not
make its way into Etch because testing was frozen before the latest
upgrade of the package. If you could do an
I hav updated to the unstable version, which have the same problem. The
outtree has a weired "inside-out" look with the most similar sequences
farther apart.
I have attached a simple infie and the resulting outtree to show what is
happening.
Yours sincerely Peter Elo
5 180
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);
