Xiao

Thanks for the suggestion. Docker is a good way to address the environment issues. I am not familiar with docker and need to learn how to use it. I will...

How many protein sequences are in the file? Are they the same species?

1. delete the old version 2. git clone the latest one 3. install according to the instructions 4. Run the command: python run_all.py -i allprotein.fa -a 20 -s 11111111 -v...

1. Integrating third-party software will involve licensing issues. I don't have such a plan. But you can use any software if they can generate hits in blast -m8 format. 2....

So true. I am not used to the latest version of blast. So, I still use old style: legacy_blast.pl blastall -p blastp ... If mcl has been installed, you can...

So “-y” is just column 3 (index2) from the m8 format? Yes. So the optimal solution is to run step 2 with pypy, and maybe step 3 with mcl parallel?...

> Hi There, Pre-declared - I am not in any sense a programer … however, Is there not a way (at least when the number of genomes is large), to...

space seed allows mismatches at specific positions in a seed. For example, -s 11011 means the 3rd position can be any character. You can find a detailed explanation at https://en.wikipedia.org/wiki/Spaced_seed#Example

It looks like an IO issue. Which OS did you run swiftortho on?

1. Why use portable-pypy: a. portable-pypy is used to install RPtyhon package. CPython is a very slow language, we used RPython to convert python code to c/c++, which significantly speeds...