-
-
Notifications
You must be signed in to change notification settings - Fork 85
/
hal-format.scroll
31 lines (28 loc) · 1.55 KB
/
hal-format.scroll
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
import ../code/conceptPage.scroll
id hal-format
name HAL Format
appeared 2012
tags binaryDataFormat
conceptDescription HAL is a graph-based structure to efficiently store and index multiple genome alignments and ancestral reconstructions. HAL files are represented in HDF5 format, an open standard for storing and indexing large, compressed scientific data sets. Genomes within HAL are organized according to the phylogenetic tree that relate them: each genome is segmented into pairwise DNA alignment blocks with respect to its parent and children (if present) in the tree. Note that if the phylogeny is unknown, a star tree can be used. The modularity provided by this tree-based decomposition allows for efficient querying of sub-alignments, as well as the ability to add, remove and update genomes within the alignment with only local modifications to the structure. Another important feature of HAL is reference independence: alignments in this format can be queried with respect to the coordinates of any genome they contain.
isOpenSource true
writtenIn cpp python make markdown c yaml r bourne-shell lisp
fileType binary
centralPackageRepositoryCount 0
repoStats
firstCommit 2012
commits 1976
committers 30
files 395
newestCommit 2024
country Unknown
originCommunity https://github.com/ComparativeGenomicsToolkit
reference https://genome.ucsc.edu/FAQ/FAQformat.html#format1
githubRepo https://github.com/ComparativeGenomicsToolkit/hal
firstCommit 2012
stars 102
forks 38
subscribers 12
created 2012
updated 2022
description Hierarchical Alignment Format
issues 82