# MAF track **TL;DR:** A MAF track shows a multiple sequence alignment of several species (or samples) against a reference genome: one row per aligned species at its true genomic position, with a coverage summary on top. It answers "how does this region compare across many genomes at once", the kind of multiz alignment UCSC publishes (e.g. the human 470-way or the _C. elegans_ 26-way). JBrowse reads three formats, MAF (tabix-indexed BED), BigMaf, and bgzipped TAF (taffy), all opened as a single track. Add one with **File → Open track**, or load a track an administrator has configured. Data-format and configuration details (adapters, the species list or Newick guide tree) live in the [MAF track configuration guide](https://jbrowse.org/jb2-staging/docs/config_guides/maf_track). This page covers what you can do once the track is on screen.
Zoomed out, each pixel summarizes the alignment beneath it. Zoom in and the per-species rows resolve into individual bases, with positions where a species differs from the reference drawn as colored marks. The features below come from two track-menu submenus: **Row coloring** picks the one way the rows are colored, and **Show...** holds the bands and overlays that layer on top of it. ## Zooming out past the alignment Every MAF format packs each block's species sequences together, so a zoomed-out query would download all of them — tens of megabytes for a single screen of a deep alignment. JBrowse blocks that with a "requested too much data" prompt. A track configured with a summary file shows presence bars there instead: one bar per species per aligned region, shaded by the summary's score, with no sequence read. Hover one to name the species, the aligned block and its score, which on a deep alignment is how to tell one row from another once the labels shrink away. Zooming back in swaps the bars for the alignment itself. Neither the coverage band nor the conservation band is drawn on the summary tier, since both are computed from the per-base alignment the tier exists to avoid reading. Pointing a track at a summary file is covered in the [MAF track configuration guide](https://jbrowse.org/jb2-staging/docs/config_guides/maf_track#the-zoom-out-tier).
## Conservation and per-row identity The **Show conservation (% identity)** band plots, at each reference base, the fraction of aligned species whose base matches the reference, a quick read of which regions are conserved versus divergent. It is computed from the alignment itself, so no extra files are needed. The **Row coloring** menu breaks the same signal out per species, so you can see _which_ genomes diverge in a region. The rows are colored one way at a time: - **Bases (SNPs vs reference)**, the default, is the per-base coloring described above. - **Identity heatmap** shades each row on a red→grey→blue ramp (red divergent, blue conserved). - **Identity X-Y plot** draws the same signal as a per-species wiggle. The heatmap and the X-Y plot draw only while you are zoomed out past base level, where individual bases are no longer legible, and zooming in swaps them back for the ordinary base coloring; uncheck **Show bases when zoomed in** to keep the plot on at every zoom level. This works on large alignments: with all ~470 species of the UCSC hg38 470-way shown at once, the heatmap gives a per-base conservation view across the full set of species. Fit-to-display-height mode takes every species into one display, so each row goes near-1px and the alignment reads as a texture, with the guide tree (dendrogram) down the left.
## Color by source chromosome **Source chromosome**, in the same **Row coloring** menu, replaces the per-base coloring with a structural view. Within each species row, the source chromosomes its blocks come from (in that species' own genome) are ranked by coverage: the row's main chromosome gets the primary color, and blocks from a different source chromosome take a contrasting accent. A row that stays one color is collinear; a row that _changes color along its length_ is drawing blocks from more than one source chromosome, an immediate flag for a translocation or rearrangement. Ranking per row keeps this readable, and a compact legend in the top-right names the scheme (main / 2nd / 3rd source). Like conservation, it is derived from the alignment with no extra data to fetch.
## Inversions (strand flips) **Show inversions (strand flips)** overlays a diagonal hatch on any block that aligns inverted relative to its own source chromosome's consensus orientation. Each block is compared to its scaffold's consensus, so an arbitrarily-oriented scaffold reads as collinear and only a genuine intra-scaffold strand flip is marked. It is an overlay, so it composes on top of the base, codon, or per-row identity rendering. ## Codon (amino-acid) view When the track has a CDS-frames file configured (a UCSC `mafFrames` annotation on the display), two coding-aware options appear. **Show CDS frames** (off by default, under **Show...**) draws a thin reading-frame-colored strip on each species' row, marking the coding exons projected onto that species so the gene structure reads vertically across the whole alignment. It is a strip drawn over whatever the rows are colored by, so it composes with any **Row coloring**. **Codon changes (amino acids)**, a **Row coloring** option, switches the per-sample rows from per-base SNP coloring to a per-codon view: every species is translated in the reference reading frame, and each codon cell is colored by how its amino acid compares to the reference: nonsynonymous changes stand out, synonymous (silent) changes get a faint tint, stop codons are flagged, and conserved codons stay clean. The residue is drawn on each codon once you zoom in far enough to read it. | Color | Name | Value | Description | | --- | --- | --- | --- | | | Nonsynonymous codon | `#e8930c` | MAF codon view: the species' amino acid differs from the reference (nonsynonymous) | | | Synonymous codon | `#3a7bd5` | MAF codon view: the codon differs from the reference but the amino acid is unchanged (silent) | | | Codon stop | `#cc2222` | MAF codon view: a stop codon | On a large alignment, narrowing to a focused set of species first (see [Selecting a subtree](#selecting-a-subtree)) keeps the per-codon columns legible, and the left sidebar redraws as the pruned guide tree.
## Tooltips Hovering any cell reads out the alignment at that position: the species, its base, and the location in that species' own genome, plus the alignment status of the neighboring blocks (e.g. a bridged gap and its size). Insertions, deletions, and bridged e-line gaps each get their own tooltip. When the CDS-frames file is loaded (in codon view, or with the strip on), the hover also shows the gene name; in codon view it shows the species' codon and amino acid next to the reference's and labels the change synonymous or nonsynonymous.
## Getting the alignment out as FASTA Drag a selection across the track and the menu that opens on release offers **View subsequences (all rows)**, or **(selected rows)** to take only the rows the drag covered. Either opens the aligned columns for that window, one sequence per species, with **Download as FASTA** and **Copy to clipboard** in its menu. That is the slice a downstream alignment viewer or tree builder wants. Without a drag, the track menu's **Launch → View subsequences (visible region)** takes the whole window and every row. The same menu offers **Show only differences**, which blanks every base matching the reference so substitutions are all that remain, plus **Include insertions**, **Single line format**, **Color background**, and **Show sample names**. A drag crossing a region boundary clips to the region it began in. ## Jumping to a species' own genome The rows of a MAF carry each species' own coordinates, so a row can be opened in its own genome. That same menu lists **one entry per species** the selection covers, naming that species' locus in its own coordinates; clicking one opens a view there. Only rows with aligned bases in the selection are listed, and only those whose sample names a genome the session can open: a sample configured with an [`assemblyName`](https://jbrowse.org/jb2-staging/docs/config_guides/maf_track#the-samples-array), or one whose id is itself an assembly the session already holds, as the strains of a [pangenome alignment](https://jbrowse.org/jb2-staging/docs/tutorials/pangenome_ecoli#whole-genome-alignment-maf-projection) are. If the session does not already hold a configured assembly, JBrowse fetches just that one at click time, which is what lets a 26-way or 470-way alignment stay navigable without every species' genome being present in the config. Past six species the entries move into a submenu. The track menu's **Launch** submenu lists the same entries over the visible window, so reaching a species' genome needs no selection. ## Comparing a species against the reference The same selection — or the visible window, from the track menu's **Launch** submenu — opens as a two-row [linear synteny view](https://jbrowse.org/jb2-staging/docs/user_guides/linear_synteny_view): **Launch synteny view, \ vs...** lists the same species, and picking one opens the reference over that species' genome with the alignment drawn between them as ribbons. The ribbons come from the MAF's own columns, so every insertion and deletion in the block is where the alignment put it, and no synteny file is involved. The reference row carries the tracks this view had open, the MAF included; the species row carries its own gene track where the session has one. ## Row layout and the species tree The sidebar at the left shows the species labels, drawn as a dendrogram when the track is configured with a Newick guide tree. - **Show... → Show tree** toggles the dendrogram and **Show row labels** the species names, and **Tree branch lengths** draws the tree to scale. - **Edit row arrangement...** reorders or hand-picks rows. - **Row height** offers squeeze-to-fit, normal, compact, and custom row heights. ### Selecting a subtree Click an internal node of the tree to filter the track to that clade, or pick a set of species from **Edit row arrangement...**. The tree then redraws as the pruned dendrogram of the kept species, so it matches the visible rows, including for a selection that is not a single clade. **Clustering → Clear subtree filter** restores all species. ### Clustering rows by identity A guide tree states how the genomes are related in general. **Clustering → Cluster rows by identity...** states how they differ over the window in view: each row is scored by how much of the window it both aligns and matches the reference at, where a stretch it does not reach at all scores zero, and hierarchical clustering over those scores gives the row order and the dendrogram. That is the ordering a cohort alignment wants. A file of one species ships no guide tree, since which haplotypes group together is a property of the locus, so its rows arrive in the order the file names them. Under an active subtree filter the run covers the visible rows only, so it resolves the structure inside the clade. The submenu names the locus a tree was computed over, since clustering reads the region in view. **Reset row order** restores the file's own order and the guide tree with it. The dialog's manual tab exports the same scores as a TSV with an R script, for clustering elsewhere and pasting the order back. ## See also - [MAF track configuration](https://jbrowse.org/jb2-staging/docs/config_guides/maf_track) - [](https://jbrowse.org/jb2-staging/docs/user_guides/linear_synteny_view) - [](https://jbrowse.org/jb2-staging/docs/user_guides/gene_track) - [](https://jbrowse.org/jb2-staging/docs/user_guides/quantitative_track) - phyloP/phastCons conservation scores as a signal track - [MAF_LARGE_BLOCKS.md](https://github.com/GMOD/jbrowse-components/blob/main/agent-docs/reference/MAF_LARGE_BLOCKS.md) — why a MAF-tabix track with very long alignment blocks is slow, and why clipping to the visible region is the wrong fix