Move BLOSUM62 substitution matrix and update scoring API #92
Conversation
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
diegozea
added a commit
that referenced
this pull request
Oct 16, 2025
* Adapt scoring functions to matrix type * Allow Real gap penalties with promotion * Fix line lengths and finalize substitution matrix
diegozea
added a commit
that referenced
this pull request
Oct 16, 2025
* Adapt scoring functions to matrix type * Allow Real gap penalties with promotion * Fix line lengths and finalize substitution matrix
diegozea
added a commit
that referenced
this pull request
Oct 16, 2025
* Adapt scoring functions to matrix type * Allow Real gap penalties with promotion * Fix line lengths and finalize substitution matrix
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Summary
ResidueSubstitutionMatrices.jlResidueSubstitutionMatrixwith a newGappedXAlphabet_pairwise_scoreandsum_of_pairs_scoreto require aResidueSubstitutionMatrixRealgap penalties and convert them to the matrix element typeNEWS.mdGappedXAlphabetinAlphabet.jland add docstring forBLOSUM62Testing
JULIA_PKG_DISABLE_DEPS_CHECK=1 julia --project -e 'push!(LOAD_PATH, "test"); using MIToSTests; MIToSTests.retest("MSA"); MIToSTests.retest("MSA")'https://chatgpt.com/codex/tasks/task_b_684c2f9dc9bc832daa7813a83e2bdb50