The Actual Modules' Code

Module code and documentation will appear here as it becomes available...

nuc_sequence_class.php

The core "nucleotide sequence" handling class.
(Nothing Available Yet)

nuc_sequence_list_class.php

For dealing with import, export, etc. of sets of nucleotide sequence objects.
(Nothing Available Yet)

prot_sequence_class.php

For Protein sequences.
(Nothing Available Yet)

prot_sequence_list_class.php

Analogous to nuc_sequence_list_class.php
(Nothing Available Yet)

Query handlers

ncbi_url_blast_class.php

Automate sending of BLAST queries to NCBI's online interface.
(Nothing Available Yet)

ncbi_eutils_class.php

For querying NCBI's EUtilities servers (Nothing Available Yet)

local_blast_class.php

Calls a locally-existing BLAST program with a query and parses the output.
(Nothing Available Yet)

Parsers

clustal_parser_class.php

Parses sequences out of .aln files produced by ClustalW and ClustalX
(Nothing Available Yet)

fasta_parser_class.php

Parses sequences from a FASTA formatted file
(Nothing Available Yet)

genbank_parser_class.php

Parse sequence and metadata from GenBank records
(Nothing Available Yet)

asn1_parser_class.php

Parse sequence and metadata from ASN.1 records
(Nothing Available Yet)

phylotree_class.php

For import, display, etc. of phylogenetic trees.
(Nothing Available Yet)

Once development gets underway with more than one person (myself) active in BioPHP development, we'll likely want to set up a project page and mailing list on Savannah or Sourceforge - to be determined depending on the opinions of other developers.

Meanwhile, as code becomes available, it will appear here as individual pages of source code for each module. Once multiple modules ar available with documentation, "tarballs" of the whole set will be here as well. Tutorials and examples will appear in their own section when they are available.