FAMSA

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Inconsistent results between Linux and MacOS

5

Hi! I recently started writing Python bindings to FAMSA ([althonos/pyfamsa](https://github.com/althonos/pyfamsa)), and after adding CI to test the code on MacOS and Linux I noticed the results were inconsistent. I thought...

althonos

compiling error on Apple M1 Pro

2

Dear FAMSA team, Check the error for apple M1 Pro (I tried both clang and home-brew gcc): *** Detecting g++ version 8 *** *** Apple M1 with NEON extensions ***...

jianshu93

famsa will replace the amino acid U with X

2

Hello! When I used famsa to alignment sequences, it would automatically replace all the amino acid U with X and keep others the same. Could you solve this problem?

LTEnjoy

Added functionality to allow profile profile alignment

1

I sometimes have alignments whose internal structure I do not wish to change, but I would like to align the two alignments to try to minimize inter-alignment distance. I wrote...

sachdved

sequence paired identity large than 100%

2

Hi , I test with follow data, but the sequence identity of matrix large than 1 . I don't know how to explan the result... `./famsa -dist_export -pid -square_matrix test.fa...

Chenglin20170390

FAMSA hangs on identical sequences

3

FAMSA (version 2.1.2- (2022-08-04) installed using conda) hangs without progress if I run it on a set of identical sequences (but different accessions). Editing a single sequence to a different...

arvestad

Segmentation fault due to `MSTPrim`

3

Hi Adam! In althonos/pyfamsa#2 @davidlougheed reported some cases of segmentation fault, some of which I traced back to the original code. For instance the sequences `["BA", "BB", "BC"]` cause a...

althonos

Git submodules for vendored libraries

1

For the vendored libraries in libs/, has the use of [git submodules](https://git-scm.com/book/en/v2/Git-Tools-Submodules) been considered for providing an easy mechanism to update dependencies to newer versions & preserve source code provenance?...

nathanweeks

I see that FAMSA allows for straightforward profile-profile alignment between MSAs using the following command: ```bash # profile-profile alignment without refining output ./famsa -refine_mode off ./test/adeno_fiber/upgma.no_refine.part1.fasta ./test/adeno_fiber/upgma.no_refine.part2.fasta pp.fasta ``` It...

PraljakReps

FAMSA (Fast and Accurate Multiple Sequence Alignment) version 2.2.2-7eb7612 (2022-10-09) S. Deorowicz, A. Debudaj-Grabysz, A. Gudys *** Error in `/home/gonzalef/FAMSA/famsa': double free or corruption (out): 0x0000000001a78660 *** ======= Backtrace: =========...

fabgonzal