Commit 8ad6e7b5 authored by omid's avatar omid
Browse files

Updating readme and todo files

parent 90e1b32e
1. Look at the Gitlab page / issues section (https://gitlab.isb-sib.ch/phylo/fastcodeml/issues)
Look at the Gitlab page / issues section (https://gitlab.isb-sib.ch/phylo/fastcodeml/issues)
......@@ -23,10 +23,14 @@ LnL0: -2393.300017592994664 Function calls: 365
p0: 0.4858354 p1: 0.5141646 p2a: 0.0000000 p2b: 0.0000000
w0: 0.0000010 k: 5.1252258
H1 Final Annotated Newick Tree (*N marks the branch N)
Final Annotated Newick Tree (*N marks the branch N)
((a001:0.169176*1,a002:0.199833*2)#1:0.254441*0,(((a003:0.005008*6,a004:0.008439*7):0.010175*5,a005:0.025300*8):0.015333*4,a006:0.130950*9):0.044605*3,a007:0.074303*10):0.000000;
Time used: 0:4
((a001:0.169176,a002:0.199833)#1:0.254441,(((a003:0.005008,a004:0.008439):0.010175,a005:0.025300):0.015333,a006:0.130950):0.044605,a007:0.074303):0.000000;
Time used: 0m:22s
Cores used: 1
===
......
- Group similar options in help (e.g. options about branch lengths)
- Unit Tests (a general test suite)
- More details in INSTALL file
to help users!!!
- For cmake, need a CMakeLists.txt example file with other compilers
- Add an option to deal with different genetic code
and maybe user own genetic code file
- Could we deal with Selenocystein and other "new" Amino acids?
- Display estimated tree (not only branch lengths) in default
output
- Promote FastCodeML in Bio* packages:
BioPerl, BioPython, BioJava, BioRuby
Open questions:
- Test if FastCodeML can avoid leaf computation
- Test what FastCodeML does with branch around root (pseudoroot)?
Does it compute only one of them in rooted tree case?
- How to force H0 computation if H1 is not significant?
Look at the Gitlab page / issues section (https://gitlab.isb-sib.ch/phylo/fastcodeml/issues)
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