...evomics.org/resources/substitution-models/nucleotide-substitution-models/
The use of maximum likelihood (ML) algorithms in developing phylogenetic hypotheses requires a model of evolution. The frequently used General Time Reversible (GTR) family of nested models encompasses 64 models with differe...
...R Input gene expression file path[required]
-m META, --meta META Input the clinical information file path that contains
the grouping[required]
-n GROUP_NAME, --group_name GROUP_NAME
Specifies the column name that contains grouping
...
... -format => 'fasta');while ( my $seqobj = $in->next_seq() ) {
# the human read-able id ofthe sequence
my $id=$seqobj->id(); # string of sequence
my $seq=$seqobj->seq();
# a description ofthe sequence
my $desc=$seqobj->desc();
# one of 'dna','rna','protein' https://www.bi...
...message and exit
-i maffile, --maf maffile
input the maf file[required]
-m metadata, --meta metadata
input metadata file path[required]
-g group, --group group
input group id in metadata file to classification
...
...ation to run. Can be uwot:Runs umap via the uwot R package; uwot-learn:Runs umap via the uwot R package and return the learned umap model;umap- learn:Run the Seurat wrapper ofthe python umap-lea...
...smu.top/treedata-book/
If you use the ggtree package suite in published research, please cite
the appropriate paper(s):
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
ggtree: an R package for visualization and annotation of phylogenetic
trees with their covariates an...
...于Artemis的DN序列可视化比较工具ampliconnoise1bl-0Programs for the removal of noise from 454 sequenced PCR amplicons去除454测序PCR扩增噪音序列arb1:1bl1-3Graphical sequence and data analysis tools.图形化序列分析工具archaeopteryx0.972.beta9M-3A phylogenetic tree viewer and...
...group_by_cluster参数，以下是官方说明
If group_by_cluster=FALSE, the dendrogram on the left is a hierarchical clustering of all non-reference cells. The first color column indicates the subdivisions ofthe dendrogram by cutting it in k_obs_groups groups. The second color column indicates t...
...O_data GO_DATA
input a GO enrichment analysis data,the data with
columns for 'category','ID','term',adjusted
p-value('adj_pval') and 'genes'[required]
-d DEG_DATA, --deg_data DEG_DATA
input the result o...
...件的时候遇到以上的问题，请问怎么解决。
Chains A, B ofthe uploaded template do not start with residue no. 1. Will be renumbered.Chain A ofthe uploaded template contains multiple unordered residues, starting at residue 623. Residue numbers must occur in ascending order. That way,...
The sequence reads were processed by Stacks version 2.6[1].We used the process_radtags function to clean the tags, discarding reads of low quality (-q), removing reads with uncalled bases (-c) and rescuing barcodes and radtags (-r). SNP calling for each individual was done using the program denov...
...stoma_floridae.protein_coding.gff3
We will discard all features that have the attribute gene_biotype with the value ne protein_coding.
Can not open Branchiostoma_floridae.gff.agat.log for printing: No such file or directoryprint() on closed filehandle $log at /share/work/biosoft/perl/perl-5.22.1/l...