package phylogenetics
Algorithms and datastructures for phylogenetics
Install
Dune Dependency
Authors
Maintainers
Sources
phylogenetics-0.0.0.tbz
sha256=8902500f9c500ee89b086563d03a4af1d4a3682fdc17ac3760da3a09b480ce4e
sha512=d3834c1236d22b30f6eb3213ccdbc34c6c1b60e20b5fb45c79e8813f87bfc4f1c913354c34781c7e6e67fbccba70ddc8c3f1751be4213e0b3ab5d5283a201c55
Description
README
README
Currently implemented:
topology tree data structure w/ branch length and indexes at leaves
parser from post-order enumeration
newick parser
data structures for bases, sequences and sequence tables;
hashtable implem for alignments (+ legacy list implem)
list implem for sequences
linear algebra functions (half wrappers around lacaml functions and half new functions);
evolution models (w/ static distribution and transition matrix diagonalization):
JC69
K80
model generation from transition matrix (poor performance so far)
felsenstein pruning w/ underflow avoidance
sequence generation from model
distribution plotting using gnuplot
tests that compare results to bio++
interface for bppml and bppseqgen for validating test results
Dependencies (9)
-
printbox
< "0.6"
- ppx_deriving
- menhir
-
lacaml
>= "10.0.2"
- gsl
-
dune
>= "2.7.0"
-
core
>= "v0.14.0" & < "v0.15"
-
biocaml
>= "0.8.0"
- angstrom-unix
Dev Dependencies (1)
-
alcotest
with-test
Used by
None
Conflicts
None
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