Computational protocol: ZPS: visualization of recent adaptive evolution of proteins

Similar protocols

Protocol publication

[…] Two input files are used: (i) a DNA alignment in FASTA format (e.g., .fasta) [see Additional files and ] using a DNA alignment software, such as ClustalX []; and (ii) a maximum-likelihood DNA tree topology (e.g., .ml.tre) [see Additional files and ] generated by PAUP* []. In the representative haplotype name, the user should only use alphanumeric characters (i.e. only decimal digits and alphabets). To allow for haplotype size/frequency-based analysis, duplicate haplotypes need to be removed in the input files, but with the user marking haplotypes with multiple representatives in the dataset by n< no. of representatives> . For example, if seqA, seqB and seqC haplotypes are identical, the user should use seqAn3 (or seqBn3 or seqCn3) as input. If there is a single representative of a haplotype, the user can use the name as it is and the program would be able to detect it as 'n1'. [...] There is one tree output – "zp_tree.dnd" where each node name (for example, 'E4-seqA-n3-2S/1N-A77D' or 'P3-seqE-n8-5S/0N') depicts (i) haplotype separation to either the External ('E') or Primary ('P') zone, with intermediate hypothetical (unresolved) nodes marked as 'H'; (ii) followed by an arbitrary number assigned to a protein variant encoded by the haplotype (e.g. 'E4' or 'P3'); (iii) original name of the representative haplotype and the user defined number of haplotypes that are identical to it in the dateset (e.g. 'seqA-n3' or 'seqE-n8'), with ZPS automatically adding '-n1' to the haplotypes with single representatives; (iv) number of synonymous(S)/non-synonymous(N) SNPs along the connecting branch (e.g. '2S/1N' or '5S/0N'), and (v) specification of amino acid changes due to the non-synonymous SNPs (e.g. 'A77D'). The ZPS output tree can be viewed with tree-presenting software, like TreeView [] or HyperTree []. The latter application also enables usage of color coding to visually distinguish different type of haplotypes and branches. Keeping HyperTree in mind, ZPS generates an additional color-code file, for the output tree file, to color-code the Primary and the External zone representatives. Two color-codes have been used: blue for all the Primary zone haplotypes that exhibit same-protein silent variability and red for all the External zone representatives. To color-view "zp_tree.dnd" in HyperTree, the user needs to 'import colors' calling "color-zp_tree.txt" file.There are two analytical outputs: "pairwise-variation.txt" and "analysis-results.txt". The former file details the positions and specific changes along each branch in the tree, while the latter presents (i) the Primary and External zone representatives; (ii) haplotype ratio (as a ratio of the number of External zone haplotypes to the total number of haplotypes in the dataset); (iii) position-wise structural mutation information, both overall and zone-based structural hot-spot frequency (as a ratio of the number of hot-spot structural mutations to the total number of structural mutations), and (iv) calculations of α and Simpson's diversity statistics []. […]

Pipeline specifications

Software tools Clustal W, SeqAn, TreeViewX, HyperTree
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Amino Acids, Nucleotides