Insect systematics: you've got to laugh, if you didn't you'd cry

In continuation from my previous post, I have now assembled 43 order level phylogenies of insects, i.e. they are based on more or less independent sources of data. The oldest study included is from 1993, so I still have my work cut out to find trees published before then especially as it becomes increasingly hard to get your hands on the articles as you go further back in time.
As more phylogenies are included, it also becomes hard to visualize this increasingly complex network on a 2D screen and I which I could explore it in a more intuitive way.

Installing tesseract command line OCR on MacOS X

Installing libpng from source:
http://kenno.wordpress.com/2006/04/20/compiling-libpng-for-mac-os-x/

fink install libjpeg, aspell, aspell-en

I will want to create my own aspell dictionary using taxonomic names:
http://www.mail-archive.com/code4lib@listserv.nd.edu/msg01545.html

Download and installing tesseract following install instructions:
http://code.google.com/p/tesseract-ocr/downloads/list

fink xpdf for pdfimages to extract images from a pdf:
>pdfimages -j LandPlants_paper.pdf LandPlantImg

To convert in imagemagick to tif for tesseract :
convert LandPlantImg.jpg -compress None test.tif

Using tesseract:
tesseract test.tif out.txt

I have now got a script to extract the names and check them against a dictionary of taxonomic names from spira.
I am thinking that using information from the article itself might provide even better results. When tesseract 2.0 comes out, there will also be a way of training the program to improve the character recognition. OCRupus also looks like an interesting program for layout detection but it doesn't work on MacOSx yet
The line extraction is proving to be much more difficult than first thought mainly because the lack of consistn format and the labelling at the nodes that get in the way of edge detection. I have tried a number of methods for cleaning up the image and bit by bit I will get there, I hope.

Branch thinning and tracking

I think I might have found a way to convert phylogenetic trees from image to nexus format through a process similar to that used in GIS map vectorization. This approach should also enable me to deal with trichotomies. The pattern matching approach that I had used previously turned out to be unsuccessful because of the many inconsistencies in tree drawing making it difficult to find a pattern that would always match a tip or a node. Line tracking offers hope!
All this would be so unnecessary if only researcher submitted their phylogenies to TREEBASE. Still, there are a number of phylogenies published prior to Treebase.