Tools

  • Gene ID conversion between Kronos and CS
  • Find wheat potential homeologs
  • Extract cDNA sequences
  • Short read de novo assembly with Velevet
  • CRISPR editing check with BWA and SAMTOOLS v2
  • CRISPR NGS editing check with HISAT2
  • Make bam files with strobeAlign
  • Shade sequence alignments with nimBoxshade
  • Shade sequence alignments with Boxshade
  • Design KASP primers with Primer3 v2.5.0
  • Convert a vcf file to SNP table
  • Call variants with exactSNP
  • Index bams with SAMTOOLS
  • Format FASTA to fixed length
  • Make bams and indel calls with Subread
  • Filter fastq files with FASTP
  • Filter multiple fastq files with FASTP
  • Make bam files with BWA and SAMTOOLS
  • CRISPR Editing Analysis v2
  • Demultiplex a Fastq File
  • CRISPR Editing Analysis
  • Call SNPs from multiple sequence alignment
  • Reverse complement of DNA sequences

    • Shade sequence alignments with Boxshade

    This tool uses Boxshade to create good looking printouts from multiple-aligned protein or DNA sequences. If you need a Desktop application, please check out pyBoxshade.

    Step 1: load alignment file


    Input format:

    Output format:

    I only know RTF, ps, eps and html formats. For the others, you need to add file extension to the output file name.

    add ruler to the alignment?
    add sequence position number?
    create consensus line?
    input is aligned DNA sequences?
    the fraction of sequences that must agree for a consensus (0-1)
    output width

    Step 2: Start shading

    Help

    Boxshade supports input files with formats:

    1. Lineup-PRETTY/Pileup-MSF file
    2. CLUSTAL .ALN file
    3. MALIGNED data file
    4. ESEE save file
    5. PHYLIP file
    6. fasta file

    And write shaded alignment to:

    • ( 1) POSTSCRIPT
    • ( 2) encapsulated POSTSCRIPT
    • ( 3) HPGL
    • ( 4) RTF (Rich Text Format)
    • ( 5) PC-screen (PCs only!)
    • ( 6) ANSI-screen (PC-version)
    • ( 7) VT100-screen (DEC-version)
    • ( 8) ReGIS-screen (25 lines each
    • ( 9) ReGIS-file (without breaks)
    • ( a) LJ250-printer file
    • ( b) ASCII file
    • ( c) FIG file (for XFIG)
    • ( d) PICT file
    • ( e) HTML file

    An edited version of Boxshade v3.3 source can be found here:
    https://github.com/pinbo/boxshade