Tools
  • Blast
  • The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

  • Gbrowse
  • GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.

  • Muscle
  • MUSCLE (MUltiple Sequence Comparison by Log- Expectation), a accurate Multiple Sequence Alignment (MSA) tool, especially good with proteins, is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options.

  • Genewise
  • GeneWise, a Pairwise Sequence Alignment tool, compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. GeneWise can provide highly accurate and sensitive predictions of gene structure.

  • Codeml
  • codeml is a part of the PAML package, which is a suite of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood (ML).

  • Positive selection analysis pipeline (PSAP)
  • PSAP is a positive selection analysis software, by simply selecting the species and analysis model, it will automaticly extract and aligment the squences, select species, finish the whole program using codeml in paml software package.

  • ExtractSeq
  • ExtractSeq is used for extracting sequence from fasta file of treeshrew genome.

  • ReverseSeq
  • ReverseSeq can convert a DNA sequence into its reverse, complement, or reverse-complement counterpart. You may want to work with the reverse-complement of a sequence if it contains an ORF on the reverse strand.

  • TranslateCDS
  • ReverseSeq can translate coding DNA sequence to protein seqeunce.