Figure 1

a: Sequence groups and characteristic residues in partitioned phylogenetic tree: Representative phylogenetic tree with sequence groups s1–s12 forming the branches of the tree. Each group may consist of one or more sequence clusters. Vertical lines divide the tree into phylogenetic distance based partitions 1–10. Nodes closest to a given partition line and located to the left of the lines define the sequence groups belonging to that partition. Root node and other nodes (A-F) up to partition 5 are shown. Groups corresponding to the different nodes are denoted as "Group n" where n is the node name. For a given partition, characteristic residues (i.e. those residues which are conserved within individual groups but not across the groups) are designated as X and color matched with their node and group names. Subscripts of X denote residue locations which are numbered with respect to a user-defined reference sequence. b: RECOVIR package GUI screenshot. Three options are shown in the orange encircled region at the top left hand corner of the GUI; File: Allows the output display to be saved in a file; Tree view: Displays genus tree in database; Help: Provides only limited help as most of the GUI options are self-explanatory through mouse attached tips. The user input and the program output parts of the GUI are indicated at the bottom. The program output part of the GUI displays the output results of the program. The user input area is divided into three parts shown using green arrows: "query sequence input", "database input" and the "output control options". These three parts correspond to the "select sequences", "database" and "view results" options in the GUI. Details of each of these parts are shown using differently colored arrows. The white board/"browse files" button (grey arrow) is used to input query sequence(s). Drop-down menus and toolbars in GUI's database input part are shown using orange arrows along with accompanying numbers; 1: "Choose a database" drop-down menu allows users to select the input target sequence genus, if known. An "unknown" option may be chosen if the genus is not known; 2: "Select a reference" allows users to select a reference sequence from the drop-down menu; 3: "View individual database sequence" option allows users to display a sequence from the selected database; 4: "View all sequences in the database" option allows users to display all the sequences in the selected database; 5: "View group members in a partition" allows users to select a partition whose all sequences within the different groups are displayed; 6: "Run" button allows program activation. The yellow arrows and their accompanying numbers in GUI's "View results" part indicate output display options: 7: "Sequence order": displays ID number of each input target sequence; 8/9: Display brief summary/details respectively of partition-wise matches of characteristic residues for an input target sequence identified by its ID in box shown using arrow '(a)'; 10: Displays details of characteristic residue matches for a chosen partition specified in box shown using arrow (b).