epa-ng

epa-ng copied to clipboard

model info error

2

**Hello, I am having trouble running epa-ng with the following error:** _INFO Selected: Output dir: ./epa_tree/ INFO Selected: Query file: query.fasta INFO Selected: Tree file: T3.raxml.bestTree INFO Selected: Reference MSA:...

RachelDanie

Support for QMaker and nQMaker from IQ-TREE?

1

Hi, Very nice software. I was wondering if you plan (or are already) supporting the new amino acid substitution models QMaker and nQMaker from IQ-TREE software? http://www.iqtree.org/doc/Estimating-amino-acid-substitution-models Thanks

michoug

Zero-length branches altered

7

Hi Firstly, thanks for developing such a great tool! I've had an odd issue occur whereby some zero-length branches in the reference tree get replaced with a branch length of...

davidemms

Error running this command

5

Hi there, I am trying to follow this [picrust tutorial](https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.1.4-beta)) After running this command: place_seqs.py -s ../seqs.fna -o out.tre -p 1 \ --intermediate intermediate/place_seqs It shows error running this command:...

edmundtayzy

Placements sensitive to outlier sequences?

3

I recently noticed that the placements of all query sequences can be affected by the presence of a small number of outlier sequences when placing onto a large tree. This...

gavinmdouglas

The model parameters under data partitioning

7

If a phylogenetic tree was generated using likelihood searches under data partitioning. How to get the model parameters? I have a reference tree that was generated by 10 partitions. My...

pyspider

Currently the epa-ng process might be killed by the system for exceeding the maximum amount of memory. This can happen with large trees / alignments. We need a strategy to...

pierrebarbera

For "weird" sequences that don't fit in the tree, or may not align correctly, or are just plain wrong, we have observed a tendency of them being placed on longer...

pierrebarbera

Provide test scripts / sanity checking for jplace

1

Especially for this early beta phase, it would be great to have a script to check the basic sanity of the output. This could allow the user to ensure some...

pierrebarbera

Split command using fasta files

2

I used mafft to align query sequences against reference msa (both in fasta format) and also the combined msa is in fasta format. Right now I have to convert everything...

koopkaup