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Sequence Family Interface User Guide

Searching for a family

 Search our collection of families, including modified KOGS and Pandit families, by one of three parameters: family name, sequence taxon name, or NCBI accession ID. Each matching entry shows the name of the family data file, a brief description, and links to view the file in plot or text form.

Uploading your own family

 You may also choose to upload your own family data file, in proper NEXUS format, for viewing. Once the upload is complete, a list of all uploaded files will be displayed. Each entry contains the name of the NEXUS file as well as links to view the file in plot or text form. This page can also be accessed by clicking the "View uploaded files" link in the upload section.

Visualizing/manipulating a family

 Clicking on the "Plot" link of a file brings up an editable image containing the tree and the sequence character matrix from the file.

This section is intended to serve only as a reference for the visualization interface . If you are new to using this interface, you may want to see our tutorial for visualizing a family for a step-by-step guide to using some of the major features.

Using the Menu Bar Mouse-over the elements in the screenshot below to see a brief description or click to see a longer description in the colored box.

  Selecting a view

Menu Bar



Reading the Image Plot Identifying Taxa by Color

grayed taxa Taxa are shown in black by default. If either "Taxonomy" or "Custom" is selected in the "Set Coloring" portion of the control panel, the taxa will be colored the appropriate color or gray otherwise.

Character Labels

char label The numeric labels located above the character matrix are read vertically, from top to bottom. For example, in the image on the left, the label inside the blue box is read as "567".

The green bars below the character labels represent weights for the columns. These only appear if the data file contains this information in an "Assumptions" block.

char label 2 Labels for the intron matrix are in vertical codon-phase notation, where the codon signifies the amino acid position and phase is that of the intron splice. The dash is represented as a pipe ( | ).

If intron history is available, a blue H will appear below the intron label. Clicking on this will bring up a menu to see either the presence probabilities as pie charts within the tree or the history plot in a separate window.

Intron Data Matrix

intron matrix While viewing the intron matrix, intron presence at a site is indicated by a plus sign (+). Absence is indicted by a dot (.).

Tree Scale

scale & reset plot button The scale for the tree is located just above the tree on the left side of the plot. This scale will not appear if the tree is in cladogram mode.



Manipulating the Tree Options for manipulating the tree can be found by clicking on the internal node of interest. The following options menu will pop up. Mouse over the options for a brief description.

Node Options

Taxa Label Options A similar option menu pops up when a taxon label is clicked. Mouse over the options for a brief description.



Node Options


Viewing a family in text form

 The "Text" link of a file presents the sequence family alignment in a textual form. The alignments are given for the intron splice positions, protein sequences, and DNA sequences; these are presented in the same format as in the plot. The taxa label of each sequence is colored by taxonomy (as defined in the NCBI taxonomy database) according to the "Taxonomy" color table, while intron splice positions are colored by phase according to the "Intron Splice Phase" color table.

Clicking on a taxa label will bring up its corresponding protein and DNA sequences, with intron splicing positions colored by phase.