progressive cactus

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+[[!meta title="Progressive Cactus is a multiple-genome aligner for the thousand-genome era."]]
+[[!tag genome alignment]]
+
+Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B.
+
+Nature. 2020 Nov;587(7833):246-251. doi: 10.1038/s41586-020-2871-y
+
+Progressive Cactus is a multiple-genome aligner for the thousand-genome era
+
+[[!pmid 33177663 desc="Aligns with cactus 2~5 genomes, in- and out-group, and reconstitutes an ancestral genome.  Recurses the phylogenetic tree progressively.  A ‘best-hit-filtering’ step is added to catch duplications that are not seen in the outgroups.  Also runs a step ‘removing recoverable chains’ to allow for corrections and mitigate error propagation.  Aligning 600 amniotes took ~2 months."]]

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@@ -8,8 +8,12 @@ see [[LAST]] for a detailed bibliography.
 
 ## Cactus
 
- - Paten and coll, ([[March 2011|biblio/21385048]]) describe _cactus_ graphs
+ - Paten and coll., ([[March 2011|biblio/21385048]]) describe _cactus_ graphs
    where nodes are sets of adjascencies and edges are aligned blocks of
    sequences.  A genome can be represented as path in these graphs.
 
+ - Armstrong and coll. ([[2020|biblio/33177663]]) describe _progressive cactus_,
+   an iterative approach where ancestral genomes are reconstituted using 2-5 pairs
+   of in- and out-group comparisons, and then progressively aligned to each other.
+
 [[!inline pages="tagged(alignment)" limit=0]]