Softwares on this page were developed to help me and my lab colleagues in our theses. I hope it is useful for you also. By the way, they are all freeware, compiled for Win95/98 and always being tested and improved.

Any comments, bug reports, suggestions, complains, etc., write me and I'll be pleased to receive your feedback. Thanks.
(IMPORTANT: please remove the 'bb' from 'alvesjmp' before sending e-mail; anti-spam measure)

LRTester v.2.0

Download it and/or Download VC6++ source code

This is a small LRT (likelihood ratio test) calculator. You provide the lnLs (calculated by PHYLIP, Puzzle, or any other phylogenetic analysis program) and some other information (whether gamma correction or invariant sites were used), some comments if you wish, and the program tells you whether your trees where or not reject, the Chi-square critical values and p-values, and all values can be saved for further use (with the comments in the beginning of the output file).

PHY2RAPD v.1.0

Download it (source code coming soon...)

This small utility converts PHYLIP 0/1 matrices (absence/ presence of characters) to RAPDistance .dat files. Useful if you do not want to enter data using RAPDistance's way, which is not that very confortable...

clus2mega v.1.0

Download it and/or Download VC6++ source code

This small utility converts Clustal multiple sequence alignments to MEGA format. Pretty much obsolete now that the new MEGA 2.1 imports other alignment formats. Useful if you do not want (or can't for some reason) install MEGA...

upperlower v.0.6b

Download it and/or Download ANSI C source code

Another very small utility. Maybe someday I merge them all in something more significant...
This one is a DOS utility that converts upper-triangular PHYLIP distance matrices (very counterintuitive to consult) to lower-triangular format with distances converted to percent similarity. Still has a major bug (names of taxa are all substituted for the name of the last taxon in the out file), but the matrix is converted correctly. It should be ready in a couple of days.
Ah, I almost forgot to mention... The source code, very short and simple, is here, so you can compile it under other OSes. I compiled it under Linux (gcc v.2.9?), and it worked just like the DOS version.

Point replacer v.2.2

Download it (source code coming soon...)

This program was developed to convert PHYLIP interleaved alignments and to calculate p-distances (% difference or similarity) for this alignment. It also gives you a file with the values used in p-dist calculatios (i.e. number of differences and number of compared sites for each pair of sequences).

Attention: version 2.2 corrects a bug that appeared when the PHYLIP file had extra blank spaces after sequence (the program repeated the last line n times; n being number of sequences). So please update your version, if you have any old one.

My problem was that I downloaded a published alignment that looked somewhat like this:

A TCATATGCTT GTCTCAAAGA TTAAGCCATG CATGTCTAAG TATAAGCTTG
B .....AA... .......... .......... .......... ..........
C .....A.... .......... .......... .......... ..........
D .....AA... .......... .......... .......... ..........
E .....--... .......... .....T.... ...---.... ....-.....
F .......... .......... .......... .......... ..........
G .......... ......T... .......... .......... ..........
H .......... .......... .......... .G........ ..........

-TTT-ATACG GCGAGACTGC GGATGGCTCA TTAAATCAGT TATAGTTTAT
.......... .......... .......... .......... ..........
.......... .....T.... .....CA... ..--...... ..........
.......TT. .......... .......... .......... ..........
.......... .......... .......... ...---.... ..........
.......... .......... .....CA... ..--...... ...GC.....
.......... .....T.... .......... ..--...... ........T.
........T. .......... .......... .......... ...G......

I needed the alignment in "normal format", that is, all nucleotides represented, and not only differences (in "point format", a conserved position is replaced by a point. It should be like this:

A TCATATGCTT GTCTCAAAGA TTAAGCCATG CATGTCTAAG TATAAGCTTG
B TCATAAACTT GTCTCAAAGA TTAAGCCATG CATGTCTAAG TATAAGCTTG
C TCATAAGCTT GTCTCAAAGA TTAAGCCATG CATGTCTAAG TATAAGCTTG
D TCATAAACTT GTCTCAAAGA TTAAGCCATG CATGTCTAAG TATAAGCTTG
E TCATA--CTT GTCTCAAAGA TTAAGTCATG CAT---TAAG TATA-GCTTG
F TCATATGCTT GTCTCAAAGA TTAAGCCATG CATGTCTAAG TATAAGCTTG
G TCATATGCTT GTCTCATAGA TTAAGCCATG CATGTCTAAG TATAAGCTTG
H TCATATGCTT GTCTCAAAGA TTAAGCCATG CGTGTCTAAG TATAAGCTTG

-TTT-ATACG GCGAGACTGC GGATGGCTCA TTAAATCAGT TATAGTTTAT
-TTT-ATACG GCGAGACTGC GGATGGCTCA TTAAATCAGT TATAGTTTAT
-TTT-ATACG GCGAGTCTGC GGATGCATCA TT--ATCAGT TATAGTTTAT
-TTT-ATTTG GCGAGACTGC GGATGGCTCA TTAAATCAGT TATAGTTTAT
-TTT-ATACG GCGAGACTGC GGATGGCTCA TTA---CAGT TATAGTTTAT
-TTT-ATACG GCGAGACTGC GGATGCATCA TT--ATCAGT TATGCTTTAT
-TTT-ATACG GCGAGTCTGC GGATGGCTCA TT--ATCAGT TATAGTTTTT
-TTT-ATATG GCGAGACTGC GGATGGCTCA TTAAATCAGT TATGGTTTAT

My problem was that I had a little less than 3000 nucleotides and 46 taxa, so manual editing was not a possibility in my case.
So you understand why I preferred to develop a program. It converts from point to normal format or from normal to point format. Point format is very useful to present alignments visually, but it can't be used as input for phylogenetic analysis programs.