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xflouris
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libpll
Phylogenetic Likelihood Library
GNU Affero General Public License v3.0
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offer parsimony functions
#50
stamatak
closed
8 years ago
2
Range based function to update a CLV
#49
pierrebarbera
closed
8 years ago
9
Getting initial branch length estimate
#48
stamatak
closed
8 years ago
0
Parsing unrooted trees as pll_rtree and vice versa
#47
pierrebarbera
closed
8 years ago
6
Alternative branch length optimization approaches
#46
ddarriba
closed
8 years ago
1
Implement a method for using the least amount of CLV vectors
#45
xflouris
opened
9 years ago
0
Per-category scalers
#44
ddarriba
closed
8 years ago
6
Potential bug with odd number of states
#43
ddarriba
closed
8 years ago
2
Makefile doesn't work on OS X
#42
ucldaniel
opened
9 years ago
14
Test case for multi-platform compatibility
#41
xflouris
opened
9 years ago
1
FASTA map incomplete for parsing protein sequences
#40
ddarriba
closed
9 years ago
0
Check for correctness of parameter in pll_partition_create()
#39
xflouris
closed
9 years ago
1
profiling of CLV and P-matrix updates
#38
stamatak
closed
6 years ago
4
BFGS pitfalls
#37
stamatak
closed
8 years ago
0
Problem when scaling is required but scaling is disabled.
#36
xflouris
closed
9 years ago
1
Thread-based parallelization
#35
stamatak
closed
6 years ago
1
Work on highly efficient parallelization
#34
stamatak
closed
6 years ago
0
low low level PLL
#33
stamatak
closed
8 years ago
4
should code be defensive about compilation with -DNDEBUG ?
#32
mtholder
opened
9 years ago
1
allocation checks in newick export
#31
mtholder
closed
9 years ago
3
Use identity matrix for p-matrix when branch length is 0
#30
xflouris
closed
9 years ago
1
Allow Win64 compatibility with MingW
#29
xflouris
closed
9 years ago
1
Add pattern weights vector to partition instance
#28
xflouris
closed
9 years ago
1
Add a prent pointer to rtree nodes
#27
xflouris
closed
9 years ago
1
One call traversal
#26
mtholder
closed
9 years ago
4
tip lookup table
#25
stamatak
closed
8 years ago
4
performance
#24
stamatak
closed
6 years ago
0
Vectorization & brief code review
#23
stamatak
closed
8 years ago
2
Change of data types
#22
xflouris
opened
9 years ago
11
Implement site weights for each partition
#21
xflouris
closed
9 years ago
1
Functionality for customized traversal of rooted and unrooted trees
#20
xflouris
closed
9 years ago
1
Fix protein-models.c testcase
#19
xflouris
closed
9 years ago
1
Remove all warnings when compiling with clang -Weverything
#18
xflouris
closed
9 years ago
1
change in API naming
#17
xflouris
closed
9 years ago
1
pll_traverse_utree
#16
xflouris
closed
9 years ago
2
Protein models validation
#15
xflouris
closed
8 years ago
7
Minor
#14
mtholder
closed
9 years ago
5
Implement subtree repeats
#13
xflouris
closed
6 years ago
5
Fix instantenous transition probability matrix to symmetric when frequencies not equal
#12
xflouris
closed
9 years ago
1
Implement simple examples
#11
xflouris
closed
9 years ago
1
Setup a wiki with current libpll documentation
#10
xflouris
closed
8 years ago
0
Discretized rate categories given an alpha parameter for the Gamma distribution
#9
xflouris
closed
9 years ago
2
Implement binary model
#8
xflouris
closed
9 years ago
1
Implement numerical scaling
#7
xflouris
closed
9 years ago
1
Implement a testing framework
#6
xflouris
closed
9 years ago
1
Implement a parser for reading binary unrooted newick trees
#5
xflouris
closed
9 years ago
0
Implement a parser for reading binary newick trees
#4
xflouris
closed
9 years ago
1
Implement protein models
#3
xflouris
closed
9 years ago
1
Implement a FASTA parser
#2
xflouris
closed
9 years ago
0
Set custom tip clv
#1
xflouris
closed
9 years ago
1
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