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phylo
fastcodeml
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a8f4ae3efab93cea48fe6c90cc61b83a4b09154d
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a8f4ae3efab93cea48fe6c90cc61b83a4b09154d
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Lucas_optimizer
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6
fix formatting
output number of aggregated codons only in verbose mode
output aggregation mode
remove nthreads message, thread number otputed twice
remove nthreads message, thread number otputed twice
fix nthreads output (correct indentations)
fix nthreads output (correct indentations)
fix minor indented formatting
fix fastcodeml output (redo 7a445d17)
retrive protoptype for the setLeaveProb & fix formatting
formatting from a7c7aee
fix multiple angular brackets and some comments formatting
fix angular braces in the style file
fix multiple angular brackets and some comments formatting
fix angular braces in the style file
apply formatting to 5e1e24c
fix format.sh to not format nlopt.h
fix format.sh to not format nlopt.h
revert nlopt formatted badly
format all the code & revert simpleopt (broken in 2589ab and c3d6fe)
code formatting scripts
format all the code
code formatting scripts
only create mMapCodonPairToDistance if aggregation is used
aggregate=2, remove 3-codon distance
find maximum minimal edit distance for s codon vector
create codon pair distance map
fix formatting in simpleopt (broken in 2589ab and c3d6fe)
re-enable tree reuse (it is disabled when aggregation is on)
make aggregation a runtime option
unrooting trees is treated (issues solved)
first version with unrooting the tree (labeling and branch numbers after
treated issue 20 (w2 issue in H1 tests)
compute H0 with multiple foregrounds (first version)
extend the ProbabilityMatrix to multiple foregrounds
treated issues:
corrected:
Merge branch 'master' of https://gitlab.isb-sib.ch/phylo/fastcodeml
remove extra tab in output for LnL0
clean.sh to clean after cmake
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