Bio::Variation name space contains modules to store sequence variation
information as differences between the reference sequence and changes
sequences. Also included are classes to write out and recrete objects from
EMBL-like flat files and XML. Lastly, there are simple classes to calculate
values for sequence change objects.
@conflict tweak from sthen
OK afresh1@
This module allows the dynamic retrieval of sequence objects
Bio::Seq from the EMBL database using the dbfetch script at EBI:
https://www.ebi.ac.uk/Tools/dbfetch/dbfetch
@conflict tweak from sthen
OK afresh1@
EMBOSS ships a lot of programs with generic names, it conflicts with
devel/pscan and also the upcoming texlive update. People who use EMBOSS
can change their PATH. Suggested by sthen@, ok edd@ sthen@
lang/python port module. I've not yet come up with a port that
would not need this and one can always set MODPY_TESTDEP to "no"
to prevent the module from touching TEST_DEPENDS.
Idea from afresh1 who pointed out the cpan module already does this.
aja "I support this move."
OK sthen@
some existing COMPILER lines with arch restrictions etc. In the usual
case this is now using "COMPILER = base-clang ports-gcc base-gcc" on
ports with c++ libraries in WANTLIB.
This is basically intended to be a noop on architectures using clang
as the system compiler, but help with other architectures where we
currently have many ports knocked out due to building with an unsuitable
compiler -
- some ports require c++11/newer so the GCC version in base that is used
on these archirtectures is too old.
- some ports have conflicts where an executable is built with one compiler
(e.g. gcc from base) but a library dependency is built with a different
one (e.g. gcc from ports), resulted in mixing incompatible libraries in the
same address space.
devel/gmp is intentionally skipped as it's on the path to building gcc -
the c++ library there is unused in ports (and not built by default upstream)
so intending to disable building gmpcxx in a future commit.
Port from maintainer Senthil Kumar M with tweaks from sthen@ and I.
ok sthen@
HMMER is used for searching sequence databases for sequence homologs,
and for making sequence alignments. It implements methods using
probabilistic models called profile hidden Markov models (profile
HMMs). HMMER is designed to detect remote homologs as sensitively as
possible, relying on the strength of its underlying probability
models.
HMMER is often used together with a profile database, such as Pfam
or many of the databases that participate in Interpro. But HMMER
can also work with query sequences, not just profiles, just like
BLAST. For example, you can search a protein query sequence against
a database with phmmer, or do an iterative search with jackhmmer.
