Table 3.
Comparison between the major steps of PHYLUCE, HybPiper, and HybPhyloMaker.
| Step | PHYLUCE | HybPiper | HybPhyloMaker |
|---|---|---|---|
| Download from Illumina BaseSpace | No | No | Yes |
| Input | Paired-end Illumina reads | Paired-end and single-end Illumina reads | Paired-end Illumina reads |
| Adapter trimming and quality filtering of reads | Yes Illumiprocessor43; pairs with both mates surviving and orphaned reads are used |
No Adapter trimming and quality filtering of reads need to be performed before using HybPiper; pairs with both mates surviving are used as input for HybPiper |
Yes Trimmomatic; pairs with both mates surviving and orphaned reads are used |
| Duplicate read removal | No | Yes (Super deduper44) | Yes (FastUniq) |
| Assembly | De novo (Velvet; ABySS45; Trinity46) | De novo (SPAdes47) | Reference-guided (Bowtie 2/BWA; OCOCO/Kindel) |
| Identification of sequences that match to the targeted sequences | Done by matching contigs to the targeted sequences (as nucleotide sequences with LASTZ); after assembly | Before assembly: done by matching reads to the targeted sequences (as peptide sequences with BLASTX); as nucleotide sequences with BWA; After assembly: done by matching contigs to the targeted sequences with exonerate |
Done by matching contigs to the targeted sequences (as nucleotide sequences with BLAT); after assembly |
| Filtering against paralogs | Yes Paralogy is indicated if a targeted locus matches multiple contigs or if a contig matches multiple targeted loci (the respective loci are excluded) |
Yes Paralogy is indicated if a targeted locus matches multiple long-length contigs (the respective loci are flagged); separation of putative paralogs possible |
No Consensus calling after the reference-guided assembly is according to majority; this results in the reconstruction of the most abundant sequence, which is considered to be the ortholog |
| Particularly suitable for exonic probe sequences | No | Yes | Yes |
| Extraction of flanking intronic regions | No | Yes | No |
| Missing data calculation | Yes | No | Yes |
| Calculation of alignment and gene tree properties | No | No | Yes |
| Flexible handling of excluding accessions and loci | Yes | No | Yes |
| Gene tree reconstruction | No | No | Yes (RAxML, FastTree) |
| Concatenation | Yes (ExaBayesa,48; RAxML; ExaMLa) | No | Yes (FastTree, ExaMLa) |
| Species tree reconstruction | No | No | Yes (ASTRAL, ASTRID, MRL) |
| Organellar phylogeny | No | Yes (from coding sequences) |
a
Input file preparation.