2 hours ago by
Hi,
I am trying to produce a .phylip file output using the ClustalO/X systems. I have a test set of 7 viral genomes (30kb) and I have run them through both the default options of ClustalO and ClustalX.
The ClustalX software seems to produce a phylip file which works with other software such as FastTree.
However, ClustalO produces a slightly different output. The output from ClustalO does not work in FastTree and I get the following error:
No sequence in phylip line TCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCAC
As you can see from the two files, there are some minor differences which could be causing the problem.
ClustalO:
MT084071.1-------------------------------------------------- TCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCAC
ClustalX
MT084071.1 ---------- ---------- ---------- ---------- ---------- TCTTGTAGAT CTGTTCTCTA AACGAACTTT AAAATCTGTG TGGCTGTCAC
Is this a bug or is there a way to get ClustalO to produce 'correctly' formatted .phylip files such as ClustalX does.
Many Thanks
