Align Exon Intron is a handy and useful utility built in order to display the alignment of exons. The program displays the exon painted in red and the alignments painted in blue by default, but it is possible to change the colors.
All you have to do is select the input files (fasta and exon) and the program will do the rest.
Align Exon Intron Crack +
You can set up a custom output file (overwrite the default output if you want):
You can also use this utility to create a custom prefix for every alignment (see details below).
This program is pretty cool, it’s not just another assembler, it performs! Many more features can be found and used in the program, including:
## Drosophila genes alignment ##
The function of the program for further information, as well as, some tips and trick:
Exon is the part of a gene that is transcribed and translated into the amino acids of a protein.
When we see this ”gene”, in fact, we are considering the exons.
You can find more explanations with the help of the website intronmap.gs.cab, where you can find information and explanations.
How to display the contents of my gene?
If you want to view or change a specific exon, you must use the context menu on the right side of the window.
How to create a prefix for every alignment?
You can create custom prefixes for every sequence alignment by selecting the sequences that you want to prefix and the prefix you want to apply.
You can see the customization options when clicking in the Settings button at the bottom of the window.
How to align (or not) a gapped sequence?
A ”gapped” sequence is a sequence that has regions with deletions.
All the sequences in a gapped alignments can be aligned with the program.
How to align positions that are more than 3 residues apart?
Align Exon Intron can also align sequences that are more than three residues apart.
This feature is useful when you have sequences that have similar regions but that are not aligned for other reasons.
How to align sequences that are not in the correct order?
Align Exon Intron also allows you to align sequences that are in the incorrect order.
This feature is useful when you want to find how an exon (or a protein) changes depending on a particular variant or if you want to align regions that are present in different genes.
How to align ”gapped” sequences?
Align Exon Intron also allows you to align sequences that have regions with deletions.
This feature is useful when you have sequences that have similar regions but that are not aligned for other
Align Exon Intron Product Key Full Download
EXECUTE: Start alignment with exon at right hand side of figure.
S/T : Stop alignment with trailing intron.
F/T : Stop alignment with leading intron.
INPUT: Select one or more input files.
OUTPUT: Display the alignment. If alignments have been stopped by (F) and (T), the respective results will be displayed. If no alignment was stopped, the results will be displayed at the end of the program.
Copyright (C) 2010 John Skelton
1/4/2016 – 02:14:25 PM
1/4/2016 – 02:23:28 PM
1/4/2016 – 02:26:40 PM
1/4/2016 – 02:29:04 PM
1/4/2016 – 02:32:07 PM
1/4/2016 – 02:40:13 PM
1/4/2016 – 02:40:50 PM
1/4/2016 – 02:41:47 PM
1/4/2016 – 02:44:46 PM
1/4/2016 – 02:49:37 PM
1/4/2016 – 02:52:45 PM
1/4/2016 – 02:54:14 PM
1/4/2016 – 02:55:01 PM
1/4/2016 – 02:56:47 PM
1/4/2016 – 03:02:16 PM
1/4/2016 – 03:03:54 PM
Align Exon Intron Incl Product Key [Win/Mac] (Updated 2022)
Exon Intron Software v4.1
Copyright (C) 2018
License: GNU GPL v3.
You can also copy and paste the program on the console in order to get in a single click a graphical alignment of the exons.
Alternatively, you can use the command line interface and specify the input files with the -i argument, which takes three arguments. First is the fasta file, second is the exon fasta and the third is the intron fasta file. (optional)
The program is developed in Java 8, and the Java Runtime (JRE) is required to execute the program. You can download the JRE from
The main methods in the program are:
This method is used to update the information displayed on the screen and it returns 1 if everything is ok and 0 if the information has to be updated again.
This method is used to read the contents of the input files using a BufferedReader.
This method is used to read the contents of the input files. You have to specify the input files with the args array of strings.
This method is used to update the output files with the result of the alignment.
This method is used to read the contents of the output files. You have to specify the output files with the args array of strings.
This method is used to read the data and put it into the array lists.
ExtractExons(double exonStart, double exonEnd, double intronStart, double intronEnd)
This method is used to read the contents of the fasta files and extract the information regarding the exons, into the start and end exon position and intron position.
UpdateTable(double exonStart, double exonEnd, double intronStart, double intronEnd)
This method is used to update the start and end exon position and intron position for each single exon
What’s New In?
It is cross-platform (Windows, Mac and GNU/Linux), free (GPL version), and it is made up of only three files (the program can do more).
You can download the Align Exon Intron from here.
Command Line Usage
The utility can be called either by the command line or as a batch file.
Using the Command Line
The Align Exon Intron utility can be run at the command line from the same directory as your input files. It takes three files (fasta and exon and alignments) as arguments and displays the results. Both files must be in FASTA format. The alignments are displayed in the same colours as the original input files.
Using a Batch File
The Align Exon Intron can also be run using a batch file. In order to do so, you can use the command line parameter -b and give it the path to a batch file. You should define the batch file with these contents:
cd ”~cprogram filesalignment_possibilitiesalign_exon_intron”
@”%~dp0exon_intron.exe” -r ”~cprogram filesalignment_possibilitiesalignments” -s ”~cprogram filesalignment_possibilitiesfasta” -e ”~cprogram filesalignment_possibilitiesexon” -f
Please note that the forward and reverse alignments are not the same when displayed as a batch file. The output is the reverse complement sequence of the original input sequence.
I am not sure whether this is considered off topic, but this site is mainly for Windows now.
I have a program which is free and has a Win and Mac version, with Linux port in the works. I have some documentation here about it.
PerformanceLab – Performance Testers – pyvpx
> PerformanceLab is a service of The New York Times Company, offering a free
> 1-hour test to every reader.
kinda creepy marketing.
hahah, no, we had them years ago and used them quite often
System Requirements For Align Exon Intron:
Windows XP / Vista / 7 / 8 / 8.1 / 10
Mac OS X 10.8 or higher
DX11 compatible graphics card
NVIDIA GeForce GTX 460 (1 GB)
AMD Radeon HD 5870 (1 GB)
ATI RADEON HD 4650 (1 GB)
Nvidia GeForce GTX 470 (1 GB)
AMD Radeon HD 4890 (1 GB)
ATI RADEON HD 4850 (1 GB)