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substitution matrix not properly reported in output

Status: Open.

#17 In Bioconductor/pwalign;

· DanielHoffmann32 opened on Mar 28, 2026

Unclear output of pwalign::mismatch

Status: Open.

#16 In Bioconductor/pwalign;

· noora-aka opened on Feb 16, 2026

stringDist using substitutionMatrix - inconsistent scores on the diagonal

Status: Open.

#15 In Bioconductor/pwalign;

· jayoung opened on Oct 22, 2025

stringDist fails on AAStringSet object containing gaps with method="substitutionMatrix"

Status: Open.

#14 In Bioconductor/pwalign;

· jayoung opened on Oct 22, 2025

pwalign results doesn't match with the Emboss needle output

Status: Open.

#9 In Bioconductor/pwalign;

· Rohit-Satyam opened on Oct 14, 2024

Is there a way to obtain the trace back matrix in align_pairwiseAlignment.c?

Status: Open.

#8 In Bioconductor/pwalign;

· peteryzheng opened on Apr 4, 2024

Terminal gaps not considered as InDel

Status: Open.

#2 In Bioconductor/pwalign;

· Close-your-eyes opened on Dec 15, 2022

vignettes "Pairwise Sequence Alignments"

Status: Open.

#3 In Bioconductor/pwalign;

· haruosuz opened on May 7, 2021

Incorrect alignment/score when using gap penalty = Inf

Status: Open.

#4 In Bioconductor/pwalign;

· traversc opened on Oct 26, 2020

alignedSubject/Pattern takes a long time to run

Status: Open.

#5 In Bioconductor/pwalign;

· LTLA opened on Jun 8, 2018

Unintuitive results with N's in pairwiseAlignment

Status: Open.

#6 In Bioconductor/pwalign;

· LTLA opened on Mar 17, 2018