BuddySuite V1.2b7

Support for earlier versions of python

BuddySuite V1.2b6

Newest V 1.2 beta release.
Full Windows support added

BuddySuite V1.2b

Beta release of major update over V1.1.

Full change log will be included in final version.

BuddySuite V1.1

General

• Update error reporting to include more function information
• Timeout usage upload and error report to prevent hangs when not connected to internet
• Catch Python2 and exit gracefully
• Add self.hash_map attributes to core Buddy classes

SeqBuddy

Upgrades

• Allow blast() function to query another sequence file instead of depending on a pre-made blast database
• Allow additional BLAST parameters to be passed in by the user
• Accept a separator character argument in make_ids_unique()
• Clean up rename() so to old ids are stored in the record description. Most output formats do not print this information, which significantly cleans up the retuned records.
• Make order_ids() numeric aware. i.e., return ['gene1', 'gene4', 'gene9', 'gene12', 'gene101'] instead of ['gene1', 'gene101', 'gene12', 'gene4', 'gene9'].
• Re-name extract_range() to extract_regions() and completely rewrite to allow a more flexible selection of which residues to return.
• New internal methods for re-mapping features to sequences that have been truncated in some way

AlignBuddy

New functions

• hash_ids
• bootstrap

Upgrades

• Un-hash all temporary files after generating an MSA if those files are being kept
• Add AlignBuddy lengths() method and modify the write() method to accept an out_format
• New internal methods for re-mapping features to alignments that have been truncated in some way
• Numeric-aware order_ids()
• Re-name extract_range() to extract_regions()

PhyloBuddy

Upgrades

• root() function now accepts regular expressions
• Hash sequence ids before running 3rd party tree building programs, then remap ids afterwards. This allows the user to name their sequences whatever they like without worry that the other software will break or rename their records.
• Add 'quiet' support to generate_tree()

BuddySuite V1.0

First full release of BuddySuite!

Following is the list of tools included in Version 1.0

SeqBuddy

delete_repeats
pull_random_record
reverse_complement
list_ids
molecular_weight
make_ids_unique
find_restriction_sites
find_pattern
order_features_alphabetically
pull_record_ends
delete_features
translate
select_frame
count_residues
ave_seq_length
merge
hash_seq_ids
group_by_prefix
translate6frames
delete_large
uppercase
pull_records
order_ids
find_CpG
rename_ids
group_by_regex
blast
order_features_by_position
lowercase
delete_metadata
guess_alphabet
reverse_transcribe
complement
clean_seq
extract_region
replace_subseq
delete_records
isoelectric_point
screw_formats
delete_small
guess_format
concat_seqs
num_seqs
transcribe
bl2seq
insert_seq
annotate
order_ids_randomly
degenerate_sequence
find_repeats
map_features_nucl2prot
map_features_prot2nucl
list_features
purge
count_codons
shuffle_seqs
back_translate

AlignBuddy

concat_alignments
trimal
reverse_transcribe
mapfeat2align
list_ids
alignment_lengths
generate_alignment
clean_seq
delete_records
translate
screw_formats
rename_ids
split_to_files
enforce_triplets
extract_range
num_seqs
transcribe
consensus
uppercase
pull_records
order_ids
lowercase

PhyloBuddy

hash_ids
rename_ids
num_tips
unroot
list_ids
show_unique
screw_formats
split_polytomies
root
print_trees
display_trees
prune_taxa
distance
consensus_tree
generate_tree

DatabaseBuddy

guess_database
live_shell

SeqBuddy v1.0 release

First release!

Version 1.0 of SeqBuddy:

• 43 command line tools
• 5 modifying flags
• BioPython V1.64 bundled with executable