Phylo - Phylogenesis library#1
Open
marco-zanella wants to merge 26 commits into
Open
Conversation
Author
|
UPDATE: The wiki was moved to the proper location: https://github.com/erpicci/Victor/wiki instead of the Phylo directory. |
Added a comment to make clearer the meaning of the way to calculate gap penalties
Author
|
Fixed memory leaks which used to lead to exponential memory usage. |
Author
|
Fixed gap extension formulae:
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Phylogesis library for the Bioinformatics 2 exam.
Implements UPGMA, NJ and ClustalW algorithm (requested by teacher), plus Fitch-Margoliash clustering algorithm, Feng-Doolitttle and Levenshtein distance metrics and Feng-Doolittle multiple sequence alignment algorithm (not requested, added as an additional effort).
Wiki available within the Phylo directory, or at https://github.com/erpicci/Victor/tree/master/Phylo/wiki
Every entity is doxygen-documented
Tested on latest Ubuntu LTS distribution (g++ version: 4.9.2)
Note: library is written in C++11 and requires g++ version >= 4.7