Orphanware collection

Original paper (Higaki et al. 2010) refers to a now defunct old Hasezawa lab web. The macros described there have become part of the Lpixel ImageJ plugins collections but it is not entirely clear how far do the presets reflect the original (although they probably do). We are therefore providing here the original 2010 versions.

• hig_skewness.txt

• hig_255counts.txt

Modern approaches to multiple sequence alignment usually focus on automated analysis of large datasets. However, manual or semi-manual multiple alignment of a few sequences still has its place, and corresponding tools are still needed. One such tool, the Multiple Alignment Construction and Analysis Workbench (MACAW), collected so far more than 960 citations, some of them as recent as 2023. Albeit last updated in 1995, MACAW provides a combination of functions unparalleled, to our knowledge, in any later freely available software, offering algorithmic searches for local blocks of sequence similarity, which may then be edited manually using an intuitive graphic user interface. This program can serve as a flexible tool for exploring protein domain organisation, but proved useful also for nucleic acid sequence analysis. Unfortunately, post-XP versions of Microsoft Windows no longer support installation of MACAW, albeit this obstacle can be overcome by a trivial modification of the installation file, which we provide together with a utility for converting MACAW-generated alignments into the FASTA format.

• Original paper (Schuler et al 1991)

• Original distribution (dead on post-XP versions of Windows) can be found here - follow the tree to pub/schuler/macaw/

• Modified archive that can be used under Win7+. No need to install, just unzip into a directory and run Macaw.exe (you might need administrator rights for this).

• Mcwreader by Radek Bezvoda - an utility to convert MACAW alignment files (*.mcw) to FASTA. Unzip into a directory and run Mcwreader.exe (Java required).

Original paper is: Hall, T.A. (1999) BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98. I cannot get hold of a copy (this volume is not even online at the publisher site, help would be appreciated!) but at least here is the manual thanks to colleagues from Masaryk University.

The latest setup file (version 7.2.6.1), OK for Windows 10, recovered from an Internet Archive copy of the now-defunct original site thanks to the Wayback Machine.