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TS404 / AlignStat

A tool for the statistical comparison of alternative multiple sequence alignments
http://AlignStat.science.latrobe.edu.au
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alignstat format #47

Open antoine4ucsd opened 3 years ago

antoine4ucsd commented 3 years ago

Hello I am interested in using alignstat to compare various alignment algorithm I tried the online version but it does not seem to work: fasta alignments are loaded but nothing happen afterward. I also installed the r package but I get an error message.... I tried loading my alignment with phylotools::read.fasta or with ape but I still have this error: Error in path.expand(file) : invalid 'path' argument In addition: Warning messages: 1: In if (tools::file_ext(alignment) == "clustal" | tools::file_ext(alignment) == : the condition has length > 1 and only the first element will be used 2: In if (tools::file_ext(alignment) == "msf" | tools::file_ext(alignment) == : the condition has length > 1 and only the first element will be used 3: In if (tools::file_ext(alignment) == "mase" | tools::file_ext(alignment) == : the condition has length > 1 and only the first element will be used

I tried with alignments in msa or fasta format... class(myFirstAlignment) [1] "MsaAAMultipleAlignment" attr(,"package") [1] "msa"

or with ref_df=phylotools::read.fasta(ref) class(ref_df) [1] "data.frame"

any suggestions?

antoine4ucsd commented 3 years ago

just following up on this. can you help with the format needed for alignstat? thank you!