Updating readme and todo files

BUGS

-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)

README

@@ -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
 
 ===

TODO

-- 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)