Ed Davis

uniqueseq.phy contains erroneous output when supplied with .nex file

4

**Error Description** Output found in the prefix.uniqueseq.phy file is not consistent with the input alignment file. There is a replication of certain amino acids multiple times rather than the input...

Incompatible prefix.nex.best_scheme.nex produced when nexus file provides alignments with * syntax

3

**Background** I generated a tree using the `-p prefix.nex` syntax with alignment files provided using the * syntax to include the entire sequence. e.g.: ``` #nexus begin sets; charset PA0005...

Feature request(s) for rehydrate

3

Brad, I don't know if this is appropriate (?) or even possible to request here. So let me know if not. I didn't see any instructions for contributions in the...

Produce robust clr matrix as output.

6

Some users would benefit from being able to access the rclr transformed values, including myself. I wrote this quick addition to return the rclr matrix and print it as tsv....

bug: NA returned by get_uid when using division_filter

3

Running into a strange bug. I'm querying some various bacterial taxa, and a handful of my taxa have conflicting genus names in the database, e.g. _Rhocococcus_. I attempted to resolve...

Compile error when STATIC_LINK=true

1

Hi there, I'm compiling using gcc 7 on centOS 7 using the `STATIC_LINK=true` flag. ```console $ make STATIC_LINK=true *** Detecting g++ version 7 *** *** x86-64 with AVX2 extensions*** make...

Fixes #37 ```console $ make STATIC_LINK=true *** Detecting g++ version 7 *** *** x86-64 with AVX2 extensions*** make -C libs/libdeflate make[1]: Entering directory '/nfs4/core/home/davised/opt/code/FAMSA/libs/libdeflate' make[1]: Leaving directory '/nfs4/core/home/davised/opt/code/FAMSA/libs/libdeflate' g++ -Wall...

[Bug] Agent response through ag-ui integration differs (hallucinates?) more

4

### Description I have an agent built with access to a knowledge base. I'm serving the LLM using vllm, and for this test, I set the temperature value to 0...