Main

Most files should be provided in a tabulated format.

Annotation

SynTView can read feature information from NCBI ptt files. These protein table files can be obtained for bacteria genomes from NCBI's ftp site: ftp://ftp.ncbi.nih.gov/genomes/Bacteria. (or use a GenBank file and a wrapper script written in Bioperl as provided here)

Below the head of FN598874.ptt file :

BDBH

The synteny information is computed from the correspondence between proteins of different organisms (Bi-Directional Best Hits – BDBH) and the conserved order of the corresponding genes along the genomes. IDs of the genes/proteins must correspond to accession numbers used in the ptt file. Names of the correspondence files are constructed with the file names of the ptt files separated by an underscore (FN598874_AE000511). The format is a tab-separated text file having the following columns:
1 id_protein_A
2 id_protein_B
3 score
4 expectency
Try a synteny data set here

Snp

The polymorphism information is computed by the mapping of several strains reads sequences against a reference genome. The SNP format is a tab-separated text file having the following columns:
1 genomic location
2 reference nucleotide
3 strain nucleotide
4 id gene (null for intergenic polymorphism)
5 strand
6 reference codon
7 strain codon
Try a SNP data set here

Phylogenetic tree

The Newick format is described here The names of the leaf nodes are the name of the ptt file.