The program also recognises distance matrices calculated by other programs from other components of sequence data, such as evolutionary distances calculated from pair-wise sequence comparisons. It reads distance matrices generated by the programs MEGA, PAUP and PHYLIP. For the current version, these externally generated matrices must be presented as upper-right or lower-left hemi-matrices or a column. Other measures of that can be converted into distances, such as the isolation dates of virus samples, may be entered for each species or gene as real numbers. If sample times are entered directly PATRISTICv1.0 will generate a matrix of time differences between the species or sequences.

The order of sequences or species represented in a tree almost always differs from the order in the original data file from which the tree was found. Hence to plot patristic distances against distances calculated by other methods or patristic distances from two trees, the program automatically reorders matrices with matching sequence or species labels. Matrices may also be edited and reordered within an editing window.

A regression is calculated from the ordered pairs of distances when two matrices are plotted against each other (Figure ​(Figure1)1) and simple statistics such as the sums of the distances are displayed. Correlation coefficients, differences and quotients between the ordered pairs of distances may also be calculated using PATRISTICv1.0, as may the mean and standard deviation of the differences or quotients, and the program has a facility to enter other formulae so that other statistics can be calculated.

Points on a plot that lie outside a chosen multiple of the standard deviation are identified by colour. Points are also automatically identified on a plot when the mouse cursor is moved over them. A zoom feature allows the user to focus on a specific part of a plot by choosing the minimum and maximum distances for the two axes which correspond to the two distance matrices. Plots of distance matrices may be inverted relative to the axes by a single mouse click. The user can also determine the scale used on the axes as well as the dot size.

Another use of patristic distances is to investigate recombinational processes. A low correlation between distances obtained from different genes may indicate a recombinational process such as horizontal gene transfer [14]. Influenza A viruses undergo a recombinational process, known as reassortment, that produces incongruities much like those produced by horizontal gene transfer, but on a smaller scale [15], and the incongruities may be identified as poorly correlated patristic distances. We detected incongruities probably due to reassortment by plotting patristic distances calculated from the neuraminidase (NA) and RNA cap-binding protein (PB2) genes of a set of influenza A virus N1 subtype isolates (Figure ​(Figure2B);2B); we found that the majority of the points lie close to the regression line and appear to increase linearly, whereas some points fall well off the line. Even when there has been no recombination, different measures of genetic difference from the same set of organisms may not correlate linearly. The rates of change in nucleotide sequences and the amino acid sequences they encode do not vary linearly because of the redundancy in the genetic code and because some sites reach a saturation point of superimposed substitutions. We demonstrated the effect by plotting patristic distances calculated from the nucleocapsid protein amino acid sequences and the equivalent nucleotide sequences of bunyaviruses (Figure ​(Figure2C);2C); the patristic distances from the nucleotide sequence tree increased at a greater rate than the equivalent patristic distances from the amino acid tree.

Operating system(s): Platform independent

Programming language: Java

Other requirements: Java 1.41 or higher http://java.sun.com