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· Alignments saved in HMT-format can be read in text, i.e. for biological data. · Alignments saved in Nexus-format can be read in the Nexus format. · Alignments saved in PIR-format can be read in PIR-format. · Alignments saved in NBRF-format can be read in text, i.e. for biological data. · Alignments saved in PAUP-format can be read in PAUP. · Alignments saved in FASTA-format can be read in text, i.e. for biological data. · Alignments saved in PHYLIP-format can be read in text, i.e. for biological data. · Alignments saved in NEXUS-format can be read in Nexus-format. · Alignments saved in PIR-format can be read in PIR-format. · Alignments saved in FASTA-format can be read in text, i.e. for biological data. · Alignments saved in PHYLIP-format can be read in text, i.e. for biological data. · Cladograms and trees can be saved in text format. · Cladograms and trees can be saved in Nexus-format. · Cladograms and trees can be saved in PIR-format. · Cladograms and trees can be saved in NBRF-format. · Cladograms and trees can be saved in PHYLIP-format. · Cladograms and trees can be saved in FASTA-format. · Cladograms and trees can be saved in PHYLIP-format. · In addition to the format, the gap or residue penalty can be saved in the alignment. · In addition to the format, the gap or residue penalty can be saved in the alignment. · In addition to the format, the gap or residue penalty can be saved in the alignment. · In addition to the format, the gap or residue penalty can be saved in the alignment. · In addition to the format, the gap or residue penalty can be saved in the alignment. · In addition to the format, the gap or residue penalty can be saved in the alignment. · In addition to the format, the gap or residue penalty can be saved in the alignment. · In addition to the format, the

ForCon PC/Windows

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ForCon

=============================================== Software ForCon is a user-friendly software for the conversion of nucleic acid and amino acid sequence alignments. Many software packages for sequence alignment and the construction of evolutionary trees have implemented their own standard of saving and reading sequence alignments. To circumvent the labourious work of manually converting alignment formats with the use of a word processor, this program was written: it converts these formats automatically. ForCon is able to convert in both ways, i.e. reading and writing the following formats (or formats used by the following software packages): · Hennig86 · NBRF/PIR · PAUP/Nexus · Parsimony Jackknifer Take ForCon for a test drive to see what it's all about! =============================================== Line 128: Line 129: == Installation == == Installation == − ForCon needs no installation. Just run the executable "converter.exe". + ForCon requires no installation. Just run the executable "converter.exe". − == Usage == + == Usage == === Enter the name of the file === === Enter the name of the file === Line 136: Line 137: === Select format (or formats used by the following software packages) === === Select format (or formats used by the following software packages) === − === Select the file to convert === + === Select the file to convert === − Select the file to be converted. All the files of the same type are converted at once. + Select the file to be converted. All the files of the same type are converted at once. === Select the program and options to be used for conversion === === Select the program and options to be used for conversion === − === Save in given format === + === Save in given format === − Save the alignment in the given format. + Save the alignment in the given format. === Save in specified format === === Save in specified format === − Save the alignment in the specified format. + Save the alignment in the specified format. === Save in specified file format === === Save in specified file

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ForCon is a simple tool for the conversion of nucleic acid and amino acid sequences alignments. The program is entirely written in Visual Basic and is very easy to use. It offers many functions including a graphical user interface, a help file and a test of the converted file. The user can choose between a hexadecimal and a graphic notation and chooses the way the sequences are aligned with respect to each other. Moreover, he can save his work in two different formats. A complete documentation is included. Usage Both input and output formats are created through a graphical user interface. Input formats A FASTA (Genbank) or NEXUS format file is needed for the input. If the sequences to align do not have any gaps, the last two lines of the file are then deleted and a "No Gaps" option is available. ForCon accepts both types of delimiters, hexadecimal and graphic. In the NEXUS format, the input can be a text file, a numeric file or a raw NEXUS file. In the case of a raw NEXUS file, the user can specify the title of the file using the --Title option. The output is saved in the FASTA format. It is possible to leave the gap code of the alignment as a parameter. If it is not set, the default value is 3. The user also has the possibility to save the alignments using the following conventions: --Gap code: For the output of the alignment, the gap code can be used (default 3). It is specified in the HXF format. It may have 3, 4, or 5 characters, for example 3-GAP, 4-GAP or 5-GAP. --Title: The alignment title can be specified with this parameter. It is a text file or a numeric file. If it is a text file, the beginning of the title is indicated with a space. The name can be used in the output as the --Title option. --Alignment code: It is specified in the HXF format. It can have 3, 4, or 5 characters. The values are 00, 01, 02 and so on. --Last line: When saving the alignment, the last two lines of the input file can be deleted. If the alignments are without gaps, the last two lines can be deleted. The sequence of the alignments is saved in the sequence of the output file. You can use ForCon to create files with different formats. For example, the output of the sequence alignment can be saved in the EMBL format (using the --EMB option) and in the FASTA format (using the --FAS option). You can also use ForCon to create an alignment and save it in the EM

System Requirements For ForCon:

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