Man pages for dongzhuoer/mcapomorphy
Molecular Classfication based on amino acid apomorphy

afroaves1_nodesub-sub-Afroaves (sup-Strigiformes) and other Afroaves
afroaves2_nodeAccipitriformes and other Afroaves
analyse_consistencyanalyse amino acide state
analyse_geneanalyse one gene for a given node
analyse_missinganalyse missing data
analyse_nodeanalyse a given node for many genes
as_char_matconvert character to char matrix
augustus_gff_to_fastaconvert gff file produced by augustus to fasta file storing...
australaves1_nodePsittacopasserae and other Australaves
australaves2_nodeFalconiformes and other Australaves
aves_nodeNeognathae and Palaeognathae
columbimorphae_nodeColumbiformes and other Columbimorphae
compare_sra_pairedcompare fastqc result of original and trimmed sequence for...
compare_sra_singlecompare fastqc result of original and trimmed sequence for...
fasta_to_gene_matconvert fasta to char matrix (with rownames)
fasta_to_nexusconvert fasta to nexus data block.
fastqc_pathreturn the full absolute path of the fastqc result
fetchdownload many webpages parallelly
fetch_assemblydownload NCBI assembly webpage for a vector of given...
fetch_genomedownload NCBI genome webpage for a vector of given id
fetch_TSAdownload NCBI WGS TSA assembly webpage for a vector of given...
file_urlreturn the url of a file on the workstation
galliformes_nodePhasianidae and other Galliformes
galloanseres_nodeGalliformes and Anseriformes
hamstr_out_to_fastaconvert hamstr output file to FASTA format
make_neoaves_node_neoaves polymotic
neognathae_nodeNeoaves and Galloanseres
node_to_groupsconvert node to groups
non_erectile_nodeSup_Gallus and Pavo
palaeognathae_nodeApterygiformes and other Palaeognathae
parse_avibaseparse wikipedia species webpage
parse_genomeparse NCBI genome webpage
phasianidae_nodetaxon (Erectile + Non_erectile) and Arborophila
pkg_fileget files in the package
psittacopasserae_nodePasseriformes and Psittaciformes
sauropsida_nodeaves and other Sauropsida
sub_aequornithes1_nodePelecaniformes and Procellariimorphae
sub_aequornithes2_nodeSphenisciformes and other sub-Aequornithes
sub_phasianidae_nodeErectile and Non_erectile
sup_aequornithes_nodesub-Aequornithes and other sup-Aequornithes
sup_gallus_nodetaxon and Gallus
sup_strigiformes_nodeStrigiformes and Cavitaves
telluraves_nodeAustralaves and Afroaves
unnest_listget the outermost list which contains more than one element
vertebrata_node1. ingroup1 2. ingroup2 3. outgroup 4. non-ingroup
view_sra_pairedview fastqc result of original SRA sequence for paired ends
view_sra_singleview fastqc result of original SRA sequence for single ends
write_paupperpare nexus file to run paup
dongzhuoer/mcapomorphy documentation built on Jan. 15, 2018, 6:53 p.m.