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Leaf Stability with branch lengths in tree file #6

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
With version 2.1, running leaf stability on a tree file with :0.0000-style 
branch lengths embedded 
fails.

Removal of the branch lengths leads to the expected output.

Original issue reported on code.google.com by ber...@gmail.com on 10 Jul 2008 at 2:36

GoogleCodeExporter commented 9 years ago 
Definitely looking into this. Would like a file to reproduce however.

Original comment by blackrim on 8 Apr 2010 at 2:47

GoogleCodeExporter commented 9 years ago 
Hi... I don't remember exactly what file I was working with at the time   :^)

These notations are generated from phyml and possibly also raxml.

I don't have a full list of bootstrap trees handy to send you, but below is a 
sample line from such a file. If you 
need a full file of these, let me know. Note there are some numbers after 
closing parentheses which are 
followed by :0.000, and others where the :0.00  is by itself.

Thanks...

((((((((((((((((mcavCyFP:0.178555,mcavGFP2:0.086873)5:0.041657,((((lhemRFP:0.048
134,scubRFP1:0.242683)4:
0.027621,tgeoRFP:0.129155)8:0.076584,mcavRFP:0.079241)9:0.116951,(Clavula:0.1609
18,dendRFP:0.17071
9)2:0.057308)3:0.040143)9:0.076262,(((Rflo:0.072510,rfloGFP:0.125453)6:0.038772,
rfloRFP:0.105618)10:0.
318775,scubGFP1:0.504033)1:0.042644)5:0.116645,Afrag:0.562926)9:0.031596,(((disc
RFP:0.036115,dis2RF
P:0.100142)10:0.242304,gtenCP:0.228090)7:0.054146,dstrCyFP:0.399790)10:0.156046)
6:0.041860,((((zoan
GFP:0.053512,zoanRFP:0.158344)5:0.033507,zoanYFP:0.061671)10:0.600110,(((((ccalO
FP1:0.062793,ccalRFP
1:0.080911)6:0.009368,ccalRFP2:0.105311)10:0.059975,((ccalGFP2:0.000000,ccalGFP1
:0.038903)9:0.02669
9,ccalGFP3:0.060133)10:0.067605)10:0.037116,ccalYFP1:0.118178)9:0.134131,(amajCy
FP:0.000000,amajGF
P:0.010405)10:0.363750)4:0.052826)6:0.042681,((alajGFP2:0.046615,alajGFP1:0.0000
00)10:0.202941,alajG
FP3:0.233923)10:0.118456)10:0.175439)8:0.103123,((equaRFP:0.262394,asulCP:0.3674
14)9:0.131047,asul
GFP:0.385017)9:0.188621)8:0.080205,((ptilGFP:0.174105,rmueGFP:0.155656)10:0.1832
14,rrenGFP:0.43604
4)10:0.344862)7:0.307267,ceriOFP:0.632345)9:0.270146,(Pontella:0.047265,PontellS
L:0.306682)10:1.45491
1)10:0.820845,(((Amacrodac:0.116772,Avictoria:0.119309)10:0.518100,clytiaGFP:0.5
63028)10:0.292738,Ant
homed:0.409564)10:0.458403)10:0.919761,HbFPcloneD:0.295642)10:0.167040,HbeeGFP5:
0.007641)6:0.00
0000,HbeeGFP4:0.003843)7:0.003834,HbeeGFP1:0.000000)0:0.000000,HbeeGFP3:0.007687
,HbeeGFP2:0.00
3823);

Original comment by ber...@gmail.com on 8 Apr 2010 at 9:02