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| Software |
| Bioinformatics and Computational Biology Software | Listings Molecule viewers Multiple Alignment Phylogenetic Analysis Integrated Sequence Tools Miscellaneous Protein Threading | |
| Integrated Sequence Tools | ||
| BioEdit | BioEditis a biological sequence alignment editor written for Windows 95/98/NT. | |
| SeqTransform last updated 5/5/00 | My sequence editing program, requires jdk1.2.1 or higher to run | |
| Listings | ||
| Phylogenetics Software | ||
| Miscellaneous | ||
| tRNAscan-SE | tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence | |
| Molecule Viewers | ||
| Cn3D 3.0 | simultaneously displays structure, sequence, and alignment | |
| Multiple Alignment | ||
| ClustalX | One of the main multiple alignment workhorses. | |
| Phylogenetic Analysis | ||
| GAML | A genetic algorithm for maximum likelihood phylogeny inference using nucleotide sequence data | |
| TreeView | Tree viewing software which reads many formats Help Manual | |
| Protein Threading | ||
| LOOPP | Does potential optimization & alignments, by seq/seq, seq/struct, struct/struct alignments. | |
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