Chemtax version 1.95 for calculating the taxonomic composition of phytoplankton populations

Full description

CHEMTAX V1.95
This program is based on CHEMTAX V1 which was produced by the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Division of Marine Research, GPO Box 1538, Hobart, Tasmania 7001, Australia (Copyright CSIRO). The MATLAB script for the original program was written by Mark Mackey (CSIRO), in association with Dennis Mackey (CSIRO), Harry Higgins (CSIRO) and Simon Wright (Australian Antarctic Division, AAD, 203 Channel Highway, Kingston, Tasmania, Australia). It was published in: Mackey, M.D., Mackey, D.J., Higgins, H.W., and Wright, S.W. (1996). CHEMTAX - a program for estimating class abundances from chemical markers: application to HPLC measurements of phytoplankton. Marine Ecology Progress Series 144: 265-283, doi: 10.3354/meps144265

The current version (CHEMTAX V1.95) was written by Chris Boucher (Barking Spider P/L), in association with Simon Wright and Harry Higgins (AAD). Peripheral software was written by Simon Wright (AAD).

It is a stand-alone program that takes input from a Microsoft Excel worksheet.

It calculates the taxonomic composition of phytoplankton populations based on pigment data and a table of the expected taxonomic composition and pigment:chl a ratios entered by the operator.

The zip folder contains Chemtax.exe, Chemtax2.dll, Testrun195.xls and CHEMTAXv195Helper7.xlm.
Also included are two Word files (Chemtax 195 Instructions.doc, and Chaxmanw.rtf, which is the manual for Version 1).The latter manual contains details on the algorithms used in CHEMTAX V1, which are unchanged, but the operating instructions in that manual are superseded by those in Chemtax 195 Instructions.doc.

Please note: CHEMTAX must not be used as a black box. It will not deduce what taxa are in the water. The user must input the expected taxa and their expected pigment composition, then CHEMTAX will calculate the contributions of each taxon to the total in each sample. It is imperative that the user understands the function of CHEMTAX, and the taxonomic distribution of pigments (including the potential ambiguities) if useful data are to be obtained.

A detailed strategy for applying CHEMTAX (and interpreting pigment data in general) is given in Higgins et al (2011). An example of combining CHEMTAX with other data is given in Wright et al (2010).

Higgins H.W., Wright S. W., Schluter L. (2011). Quantitative Interpretation of Chemotaxonomic Pigment Data, Chapter 6, Phytoplankton Pigments: Characterization, Chemotaxonomy and Applications in Oceanography, Suzanne Roy, Einar Skarstad Egeland, Geir Johnsen and Carole Anne Llewellyn (eds.) Cambridge University Press.

Wright, SW, van den Enden, RL, Pearce, I, Davidson, AT, Scott FJ, Westwood, KJ (2010). Phytoplankton community structure and stocks in the Southern Ocean (30 - 80 degrees E) determined by CHEMTAX analysis of HPLC pigment signatures. Deep-Sea Research II 57, 758-778

Registration:

After downloading the files, please email the enclosed registration form to [email protected] with CHEMTAX in the title

Lineage

Progress Code: completed

Statement: CHEMTAX distribution: There is an unresolved issue with V2 which our developer was unable to address before the end of contract. V1.95 is offered in the meantime. Note that the "Solve" routine works fine, but the "Convergence" routine has a bug and shouldn't be used. The package includes Excel macros that handle V1.95 data - tabulating the results from multiple runs (to aid choosing the best result) and normalizing the ratios for each taxon (to assess validity of the results) . This adds much of the V2 power, but it's nowhere near as elegant. Development of CHEMTAX V2 is in limbo due to loss of staff. A new algorithm has been developed and it is planned to release it as open source but development now rests entirely with [email protected], who is semi-retired. Please note: Some users have encountered the following error when trying to use CHEMTAX for the first time: "Component 'comdlg32.ocx' or one of its dependencies not correctly registered: a file is missing or invalid" The file is a Windows component that is needed for running VisualBasic files, but is missing from some installations. Users had success after downloading the file from this site: http://www.bioinformatics.org/snp-tools-excel/install_comdlg32.htm 2017-07-24 - an update to the download file was made available. The application itself did not change, but some example files, instructions and a macro suite were added to the download directory. 2017-11-06 - an updated CHEMTAX file was provided by Simon Wright.