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As already discussed, current tip-inner functions are not efficient for state-rich models (e.g. AA data). In fact, performance was even worse than inner-inner even for reasonably long sequences (-1000…
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Current definition:
``` C
/* multiple sequence alignment */
typedef struct pll_msa_s
{
int count;
int length;
char ** sequence;
char ** label;
} pll_msa_t;
```
`count` and `length` are comp…
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We should do profiling runs for full tree traversals to determine how much time is spent in P-matrix and CLV updates and if it would be worthwhile to further optimize the p matrix calcs.
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@bwelle @antonszilasi @chiensiTB
you are now all members of a new team: @ladybug-tools/build-well
***
Am I correct in thinking that this validator is not that helpful at our current stage o…
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## People to be invited
- [ ] Andreas Harth, Karlsruhe Institute of Technology
- [ ] Sandro Hawke, Massachusetts Institute of Technology
- [ ] Lalana Kagal, Massachusetts Institute of Technology
-…
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I believe we should clean up the root directory of the project since it seems that there are a number of files that got there by accident or are no longer really needed.
Would like to get some feed…
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Hi Diego,
I was able to compile foreseqs in a CentOS machine with 64GB of memory. The binary runs fine with the example dataset but I encounter a segmentation fault before any text is written on…
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The parameter optimization routine may evaluate non-sensible parameters that cause the pmatrix to be close to the identity matrix but, due to numerical underflow, cause some cells to have small negati…
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The PHYLIP parser currently implemented in libpll has several shortcomings:
1. Performance: on large alignments, libpll PHYLIP parser is 50-100 times slower compared to RAxML/genesis, e,g,:
```
5…