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readTrees branch length reading bug #136

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ssolo opened this issue Sep 29, 2018 · 0 comments
Open

readTrees branch length reading bug #136

ssolo opened this issue Sep 29, 2018 · 0 comments

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@ssolo
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ssolo commented Sep 29, 2018

Non zero branch length are read as zero.

e.g. this tree:
(((((((((((((P036_Human:1.13508e-06,P035_Chimp:9.41569e-07):7.19146e-07,P034_Gorilla:1.44166e-06):1.58262e-06,P033_Orangutan:2.61255e-06):3.20482e-06,P032_Rhesus:5.32134e-06):4.10426e-06,P031_Marmoset:1.43264e-05):1.80946e-05,P030_Tarsier:4.02052e-05):5.21827e-06,(P029_Mouse_lemur:3.31786e-05,P028_Bushbaby:4.3736e-05):1.15486e-05):4.65678e-06,P027_Tree_shrew:4.39095e-05):2.6976e-06,(((((P026_Rat:2.42636e-05,P025_Mouse:2.38935e-05):9.25348e-05,P024_Kangaroo_rat:9.65724e-05):1.86136e-05,P023_Guinea_pig:8.84517e-05):8.85101e-06,P022_Squirrel:5.07127e-05):9.36665e-06,(P021_Pika:6.09761e-05,P020_Rabbit:4.20026e-05):4.16715e-05):6.58083e-06):7.18835e-06,((((P019_Microbat:4.65155e-05,P018_Megabat:2.95788e-05):1.11789e-05,((P017_Cat:2.69545e-05,P016_Dog:2.42869e-05):1.8638e-05,P015_Horse:2.54788e-05):2.47183e-06):1.88827e-06,(P014_Alpaca:2.84404e-05,(P013_Pig:3.37522e-05,(P012_Cow:3.25738e-05,P011_Dolphin:1.27459e-05):6.77014e-06):4.31303e-06):1.20045e-05):4.03013e-06,(P010_Common_shrew:0.000135757,P009_Hedgehog:0.000104649):4.04484e-05):6.05599e-06):1.19182e-05,((P008_Sloth:2.97787e-05,P007_Armadillo:4.34446e-05):2.22952e-05,((P006_Elephant:3.30822e-05,P005_Rock_hyrax:5.56953e-05):2.46276e-05,P004_Tenrec:0.000105711):2.44351e-05):1.08933e-05):0.000250908,(P003_Wallaby:9.81598e-05,P002_Opossum:0.000104851):0.000279013):0.000524982,P001_Platypus:0.000524982):0;

is read as this (see e.g. node with index=25)

(((((((((((((P036_Human[&index=36]:0.000001,P035_Chimp[&index=35]:0.000001)[&index=37]:0.000001,P034_Gorilla[&index=34]:0.000001)[&index=38]:0.000002,P033_Orangutan[&index=33]:0.000003)[&index=39]:0.000003,P032_Rhesus[&index=32]:0.000005)[&index=40]:0.000004,P031_Marmoset[&index=31]:0.000014)[&index=41]:0.000018,P030_Tarsier[&index=30]:0.000040)[&index=42]:0.000005,(P029_Mouse_lemur[&index=29]:0.000033,P028_Bushbaby[&index=28]:0.000044)[&index=43]:0.000012)[&index=44]:0.000005,P027_Tree_shrew[&index=27]:0.000044)[&index=45]:0.000003,(((((P026_Rat[&index=26]:0.000000,P025_Mouse[&index=25]:0.000000)[&index=46]:0.000132,P024_Kangaroo_rat[&index=24]:0.000132)[&index=47]:0.000019,P023_Guinea_pig[&index=23]:0.000150)[&index=48]:0.000009,P022_Squirrel[&index=22]:0.000051)[&index=49]:0.000009,(P021_Pika[&index=21]:0.000127,P020_Rabbit[&index=20]:0.000127)[&index=50]:0.000042)[&index=51]:0.000007)[&index=52]:0.000007,((((P019_Microbat[&index=19]:0.000047,P018_Megabat[&index=18]:0.000030)[&index=53]:0.000011,((P017_Cat[&index=17]:0.000027,P016_Dog[&index=16]:0.000024)[&index=54]:0.000019,P015_Horse[&index=15]:0.000025)[&index=55]:0.000002)[&index=56]:0.000002,(P014_Alpaca[&index=14]:0.000028,(P013_Pig[&index=13]:0.000034,(P012_Cow[&index=12]:0.000033,P011_Dolphin[&index=11]:0.000013)[&index=57]:0.000007)[&index=58]:0.000004)[&index=59]:0.000012)[&index=60]:0.000004,(P010_Common_shrew[&index=10]:0.000136,P009_Hedgehog[&index=9]:0.000136)[&index=61]:0.000040)[&index=62]:0.000006)[&index=63]:0.000012,((P008_Sloth[&index=8]:0.000030,P007_Armadillo[&index=7]:0.000043)[&index=64]:0.000022,((P006_Elephant[&index=6]:0.000033,P005_Rock_hyrax[&index=5]:0.000134)[&index=65]:0.000025,P004_Tenrec[&index=4]:0.000159)[&index=66]:0.000024)[&index=67]:0.000011)[&index=68]:0.000251,(P003_Wallaby[&index=3]:0.000166,P002_Opossum[&index=2]:0.000166)[&index=69]:0.000279)[&index=70]:0.000525,P001_Platypus[&index=1]:0.000525)[&index=71]:0.000000;

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