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Biopython can read and write to a number of common sequence formats, including FASTA, FASTQ, GenBank, Clustal, PHYLIP and NEXUS. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others.
FASTA, GenBank, EMBL, Newick: Proprietary, freeware, arb license, open modifiable source No Linux, Mac OS (homebrew) Official website: Base-By-Base No MUSCLE UPGMA, NJ, complete and single linkages, WPMGA Visual summary, percent identity tables, some integrated advanced analysis tools Genbank, FASTA, EMBEL, Clustal, base-by-base files
FASTA: Local search with fast k-tuple heuristic, slower but more sensitive than BLAST: Both: GGSEARCH, GLSEARCH Global:Global (GG), Global:Local (GL) alignment with statistics: Protein: Genome Magician Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ). DNA: Hepperle D (www.sequentix.de ...
Biopython: Python language toolkit Cross-platform: Biopython [1] Open Bioinformatics Foundation: BioRuby: Ruby language toolkit ? GPL v2 or Ruby: Open Bioinformatics Foundation: BLAST: Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platform: Public domain
A DNA dot plot of a human zinc finger transcription factor (GenBank ID NM_002383), showing regional self-similarity. The main diagonal represents the sequence's alignment with itself; lines off the main diagonal represent similar or repetitive patterns within the sequence. This is a typical example of a recurrence plot.
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an online tool for phylogenetic tree view (newick format) that allows multiple sequence alignments to be shown together with the trees (fasta format) EvolView [3] an online tool for visualizing, annotating and managing phylogenetic trees IcyTree [4] Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks