> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods.md).

# Tasks - Bioinformatics Methods

- [UCSC Genome Bioinformatics](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics.md)
- [Interacting with the UCSC Genome Browser](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/interacting-with-the-ucsc-genome-browser.md)
- [Obtaining DNA sequence from the UCSC Database](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/obtaining-dna-sequence-from-the-ucsc-database.md)
- [Obtaining genomic data from the UCSC database using table browser queries](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/obtaining-genomic-data-from-the-ucsc-database-using-table-browser-queries.md)
- [Filtering table browser queries](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/filtering-table-browser-queries.md)
- [Performing a BLAT search](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/performing-a-blat-search.md)
- [Creating Custom Tracks](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/creating-custom-tracks.md)
- [UCSC Intersection Queries](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/ucsc-intersection-queries.md)
- [Viewing cross-species alignments](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/viewing-cross-species-alignments.md)
- [Galaxy](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/galaxy.md)
- [Intro to Galaxy](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/galaxy/intro-to-galaxy.md)
- [Galaxy NGS Illumina QC](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/galaxy/galaxy-ngs-illumina-qc.md)
- [Galaxy NGS Illumina SE Mapping](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/galaxy/galaxy-ngs-illumina-se-mapping.md)
- [Galaxy SNP Interval Data](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/galaxy/galaxy-snp-interval-data.md)
- [Editing and annotation gene structures with Argo](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/editing-and-annotation-gene-structures-with-argo.md)
- [GeneGO MetaCore](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore.md)
- [GeneGo Introduction](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/genego-introduction.md)
- [Loading Data Into GeneGO](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/loading-data-into-genego.md)
- [Data Management in GeneGO](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/data-management-in-genego.md)
- [Setting Thresholds and Background Sets](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/setting-thresholds-and-background-sets.md)
- [Search And Browse Content Tab](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/search-and-browse-content-tab.md)
- [Workflows and Reports Tab](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/workflows-and-reports-tab.md)
- [One-click Analysis Tab](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/one-click-analysis-tab.md)
- [Building Network for Your Experimental Data](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/genego-metacore/building-network-for-your-experimental-data.md)
- [Functional Annotation of Gene Lists](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/functional-annotation-of-gene-lists.md)
- [Multiple Sequence Alignment](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/multiple-sequence-alignment.md)
- [Clustalw2](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/multiple-sequence-alignment/clustalw2.md)
- [Phylogenetic analysis](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/phylogenetic-analysis.md)
- [Neighbor Joining method in Phylip](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/phylogenetic-analysis/neighbor-joining-method-in-phylip.md)
- [Microarray data processing with R/Bioconductor](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/microarray-data-processing-with-r-bioconductor.md)