However, you only see one difference when you look at the present day sequences. See the documentation for details. Ignore gaps in alignment With this option, any alignment positions where ANY of the sequences have a gap will be ignored. This means that 'like' will be compared to 'like' in all distances. The disadvantage is that you may throw away much of the data if there are many gaps.
All images have same size.
Width and height of the images may be set from 320 to 2000 and 240 to 1500 pixels, respectively. Defaults are 640 and 480. This option restrains the difference so that very short branches are plotted with length only at factor times less than maximum plotted. Such branches are dispayed in orange color. July 29, 1999.