This is a test version of Biostars. For the public version, visit https://www.biostars.org.
AAI matrix with compareM

Hi everybody, I’m trying to make an average amino acid identity matrix using the compareM code provided by GitHub for Ubuntu. I also installed prodigal and diamond. However when I run the ubuntu program tells me that it does not find any genome in the input folder, asking to check the file extension to verify that they are in fast format. I checked several times with the ls *.fasta and head commands and there are no errors. Does anyone know what the problem might be or have any advice for me? thanks in advance

aai matrix
• 604 views • link
written by anna • anna

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Tool: New tool for narrowing difficult missense variant shortlists
    written by Lara Finley • Lara Finley
    We’ve been building a new tool for the annoying stage of variant analysis where you’ve already run the usual annotations, filtered on frequency, checked ClinVar, …
  • dbSNP VCF file compatible with GRch38.p14
    written by Kelly • Kelly
    Hello Bioinformagicians, I’m a somewhat rusty terminal-based processes person with some variant calling experience in my prior workspace. I am not used to working from …
  • Struggling with protein context of Annovar output
    written by papp.benjamin.t • papp.benjamin.t
    Hi, Im having some troubles extracting the protein sequences of missense mutations from annovar output files. I would like to create all of the **possible …
  • Amino Acid identity matrix help
    written by Confused_human • Confused_human
    Hello everyone, I have a dataset of 4000 protein fasta sequences with me. Example dataset: ``` >Acaryochloris_marina_peg_1945 MNILAVIPARYQSQRFPGKPLVMLDERPMVQWVYEAAKSCDFFQDAVVATDSDKIADCVKGFGGKVVMTRDDHLTGTDRVAEVAGFYDDMDVVVNVQGDQPFVTPEALEQLVRPYREGERPEMTTLGCPLDMDEDYASPNAVKVLCDRNGHALYFSRSPIPYFRTQGTVPVYHHLGLYAFRHDFLMQYSQLEPTPFETCEGLEQLRVLEYGYAIKVCQTQKAAIEINTPEDLVKAQLFIQQGMTS >Acetivibrio_clariflavus_peg_3972 MRTGVIVQTRMGSSRLPGKVMIDICGKPVIEHVIDRLKMSKVLDDIIIATTTSVKDKIIVEQAKRNGVKWFCGSEEDVLSRYYYAARENRLSTVVRVTSDCPLIDPVILDEIVEFYKKNDYLLVTNAGNILEYRTYPRGLDVEVFSFDILEKAFYSAKKPYQREHVTPYIYETYENKIYYYKNNINLSKYRWTLDTEEDLKLISIIFNNFYYKYGRNFGFKDILKFIQSNPQLSKINEHIEQKKIG >Acetivibrio_clariflavus_peg_4060 MKILFTICGRKGSKGVKSKNIKTFLGFPLAFYTASFIDLFIKRNNWVDSDIVLNTDSENLIDLFKNKLNMPIEIIERDPELAKDYVPKISVIKNCYDVMVERKKVSYDIVIDLDITSPLRRLRDLQSLIEKKLNSNADVVFSVTSARRNPYFNMVKKGENGYERVIESSFNARQEAPNVFDINGSMYAYSPDFLKSGKGLFDGICDIIEMRDTAVLDIDHENDFELMEVIAKYLYSSDNEYNCIRENINNILLKD >Acetivibrio_saccincola_peg_0278 MKKVVAIIQARMGSTRLPGKVMKNLCGKTVLAHDIERVRQSKYIDEIVIATTKFKEDDIILREALENGAKVYRGSEDDVLRRYYEAAKENKADVIVRITSDCPLIDPFIVDEVIKVYLNSNYDLVTNAGIYPENRTYPRGLDVEVFSFDILKKAFQEAKEMYQREHVTPFIYENSKNIYYYKNDIDYSKYRWTLDTEEDYKLIEIIYKSFIKESIIFILMIF*SCLIICQSYLKLIKMCNKKLSVD >Acetivibrio_saccincola_peg_0286 …
  • Can't find fstat() and pairwise.fstat()
    written by Noctiluca • Noctiluca
    Some months ago I run a calculation of the F-statistics on a set of SNP data from contiguous populations using the fstat() from hierfstat. I …
  • Tutorial: Building mosdepth on macOS
    written by ATpoint ATpoint
    This is just a tiny tutorial on how to build [mosdepth][1] on Mac. There is currently no version for Mac available at conda (hope that …
  • Calculating Average Amino Acid Identity (AAI) using CompareM
    written by charles.bridges charles.bridges
    Hi all, I'm trying to calculate Average Amino-acid Identity (AAI) between a set of ~15 genomes. A program called CompareM (https://github.com/dparks1134/CompareM from the same set …
  • Trouble with GenomicFeatures Package
    written by MarjoryMollusc • MarjoryMollusc
    I have installed GenomicRanges, the dependency before-hand and then have tried to install GenomicFeatures. Both appear to say that they have successfully been installed however …
  • Basic SAMtools tutorial
    written by statfa statfa
    HI, I need some help to start working with SAMtools. As a beginner with biostatistics background, it is my first time that I'm using Linux …
  • Genscan Doesn'T Run
    written by Ken • Ken
    Hi, I am migrating things from our old server to new servers. The genscan works fine in the old server but it doesn't work in …