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Perl scripts

These scripts are Open Source - cut, copy and modify to your heart's content, but an acknowledgement would be kind.

ape2map

A perl script to create pretty graphics maps from annotated GenBank files - as from the recommended software ApE: A Plasmid Editor. This program is the upgraded version of ape2svg, which is included below in case of compatibility issues. It uses PerlMagick (a perl interface for the brilliant ImageMagick) to render to a large variety of formats.

The maps on the vectors resource page were generated with these script. You'll need to be comfortable running scripts from a terminal to use it. Microsoft Windows users will need to install ActivePerl.

ape2svg

A perl script to create pretty scalable vector graphics (SVG) images from annotated GenBank files. The predecessor to ape2map above, which is the recommended script.


ImageJ macros

This section provides tools to aid in the analysis of flagellar ultrastructure and beating. The files are macros for the fantastic Open Source image manipulation and analysis software ImageJ. A huge amount of extra functionality is freely available for the program in the form of plugins. Macros are similar, but generally quicker to write and not quite as slick looking. You can do all of the tasks provided by these macros the long way around, but they should speed things up considerably.

These scripts are Open Source - cut, copy and modify to your heart's content, but an acknowledgement would be kind.

Axoneme ellipse correction

Corrects transverse axonemal EM sections for elliptical deformation caused by cut angle being not exactly orthogonal to the longitudinal axis of the axoneme, as described in Gadelha et al. (2006) JCS 119:2405-13. Macro performs non-linear least-squares fit of doublet positions to a deformed nonagon, corrects deformation and normalises axoneme to specified size. This allows cross-sections to be directly superimposed such that quantitative analysis and true angle measurements can be made.

Beat analysis toolkit

A set of tools for extracting data from movies of flagellar/ciliary beating and for the easy implementation of the "swimming on the spot" transformation (removal of cell translational motion without loss of beat information) as described in Gadelha et al. (2007) CMC 64:629-43.