Aligner¶
- class pyfamsa.Aligner¶
A single FAMSA aligner.
- __init__(*, threads=0, guide_tree='sl', tree_heuristic=None, medoid_threshold=0, n_refinements=100, keep_duplicates=False, refine=None)¶
Create a new aligner with the given configuration.
- Keyword Arguments:
threads (
int
) – The number of threads to use for parallel computations. If 0 given (the default), useos.cpu_count
to spawn one thread per CPU on the host machine.guide_tree (
str
) – The method for building the guide tree. Supported values are:sl
for MST+Prim single linkage,slink
for SLINK single linkage,upgma
for UPGMA,nj
for neighbour joining.tree_heuristic (
str
orNone
) – The heuristic to use for constructing the tree. Supported values are:medoid
for medoid trees,part
for part trees, orNone
to disable heuristics.medoid_threshold (
int
) – The minimum number of sequences a set must contain for medoid trees to be used, if enabled withtree_heuristic
.n_refinements (
int
) – The number of refinement iterations to run.keep_duplicates (
bool
) – Set toTrue
to avoid discarding duplicate sequences before building trees or alignments.refine (
bool
orNone
) – Set toTrue
to force refinement,False
to disable refinement, or leave asNone
to disable refinement automatically for sets of more than 1000 sequences.
- align(self, sequences)¶
–
Align sequences together.