Volume 17 Supplement 8
Selected articles from the 11th International Symposium on Bioinformatics Research and Applications (ISBRA '15): bioinformatics
PnpProbs: a better multiple sequence alignment tool by better handling of guide trees
 Yongtao Ye^{1},
 TakWah Lam^{1} and
 HingFung Ting^{1}Email author
https://doi.org/10.1186/s1285901611217
© The Author(s) 2016
Published: 31 August 2016
Abstract
Background
This paper describes a new MSA tool called PnpProbs, which constructs better multiple sequence alignments by better handling of guide trees. It classifies sequences into two types: normally related and distantly related. For normally related sequences, it uses an adaptive approach to construct the guide tree needed for progressive alignment; it first estimates the input’s discrepancy by computing the standard deviation of their percent identities, and based on this estimate, it chooses the better method to construct the guide tree. For distantly related sequences, PnpProbs abandons the guide tree and uses instead some nonprogressive alignment method to generate the alignment.
Results
To evaluate PnpProbs, we have compared it with thirteen other popular MSA tools, and PnpProbs has the best alignment scores in all but one test. We have also used it for phylogenetic analysis, and found that the phylogenetic trees constructed from PnpProbs’ alignments are closest to the model trees.
Conclusions
By combining the strength of the progressive and nonprogressive alignment methods, we have developed an MSA tool called PnpProbs. We have compared PnpProbs with thirteen other popular MSA tools and our results showed that our tool usually constructed the best alignments.
Keywords
Multiple sequence alignment Guide trees Phylogenetic treesBackground
Constructing multiple sequence alignments (MSA) is an important problem in Bioinformatics. For sequences with sufficiently high similarity, there exist many MSA tools that can produce good alignments, but for sequences with similarity below 30 %, no tools have satisfactory performance. However, these sequences are also of great interest to biologists because even though they have low similarity, many of them have similar secondary and tertiary structures. This paper introduces a new software tool PnpProbs. It can construct significantly better alignments for sequences with low similarity, and it also improves the alignments for general input.

Determine the substitution scores for pairwise sequences based on some pairHidden Markov model(s), and then refine the scores to make them consistent with all input sequences.

Construct a guide tree and based on it align the input sequences progressively to generate the multiple sequence alignment.

Refine the alignment given by Stage (2) to a better alignment for the final output.
The major difference between MSAProbs and GLProbs is in the first stage: MSAProbs uses a single model to determine the substitution scores, while GLProbs determines the scores adaptively. GLProbs first estimates the similarity of the input sequences by computing its average PID (percent identity), which is defined as follows: the PID of two sequences is the percentage of identical columns in their optimal (pairwise) alignment, and the average PID of a sequence family is the average of the PIDs of every pair of sequences in the family. If the input’s average PID is high, GLProbs uses the global pairHidden Markov model (pairHMM) to determine the scores; otherwise, it uses some local pairHMMs.
We have made thorough comparisons between GLProbs and a dozen other leading MSA tools, and GLProbs had the highest accuracy in many of the comparisons (see [1] for more details of our evaluation of GLProbs).
In this paper, we have some ideas for improving GLProbs, and we implement them by developing the alignment tool PnpProbs. We have tested PnpProbs extensively on three benchmark databases BAliBASE [3], OXBench [4], and SABmark [5], and in Section “Benchmark comparison”, we compare its performance with 13 leading multiple sequence alignment tools, including 10 using the progressive method: ClustalW [6], Clustal Ω [7], TCoffee [8], MAFFT [9], MUSCLE [10], ProbCons [11], CONTRAlign [12], Probalign [13], MSAProbs [2], GLProbs, and 3 using the nonprogressive method: Alignm [14], PicXAA [15], and DIALIGNPFAM [16]. PnpProbs’ performance is significant better, specially for distantly related sequences. For example, for families of sequences in OXBench with similarity from 0 to 20 %, PnpProbs achieved an improvement (in TC score) over ClustalW by 36.5 %, over PicXAA by 12.9 % and GLProbs by 8.4 %.
We have also evaluated the performance of PnpProbs on phylogenetic inferencing over two benchmarks, namely YuleHarding tree simulated data [17] and SABmark empirical data [5]. In Section “Phylogenetic analysis”, we compare PnpProbs with five other MSA tools, namely GLProbs, MSAProbs, PicXAA, MUSCLE and ClustalW, and our results showed that the phylogenetic trees generated from the outputs of PnpProbs are closer to the model phylogenetic trees than those constructed from the five other MSA tools.
For verification of our results, all test data can be accessed from [17, 18], and PnpProbs can be downloaded via the link https://github.com/ytye/PnpProbs.
Ideas for improving GLProbs
We observe some new structural properties and believe that by exploiting them we can further improve GLProbs’ accuracy in general, and improve its accuracy significantly for sequences with low similarity. We focus on improving the second stage of GLProbs. Based on the substitution scores given in Stage 1, this stage determines a guide tree, which is supposed to capture the phylogeny relationship of input sequences. Then, it generates an MSA by performing profiletoprofile alignment according to the order suggested by the guide tree. Unlike GLProbs, we will use an adaptive approach to construct the guide trees. We classify the input sequences into two types: (i) distantly related sequences, whose similarities (or more precisely, average PID) are smaller than some threshold (as suggested by our study in Section “Nonprogressive alignment for distantly related sequences”, we set it to be 18 %), and (ii) normally related sequences, whose similarities are no smaller than the threshold. PnpProbs handles these two types of sequences differently.
(†) Their sequences have a number of conserved regions over which the sequences are very similar, and the sequences are very different elsewhere.
 (i)
The average PID cannot help us discover (†), but the standard deviation can. As shown in Fig. 1, while F and G have the same average PIDs, the standard deviation of their PID’s are quite different: for F, the PIDs of its sequence pairs are 0.5 (1st and 2nd sequences), 0.5 (2nd and 3rd), and 0 (1st and 3rd), and their standard deviation is significantly greater than 0, and for G, the PIDs of its sequence pairs are all equal to 0.33 and their standard deviation is 0. This is not surprising because the sequences in G are identical over the two conserved regions, and are totally different elsewhere. In general, if a family has small standard deviation of PID, it may have structure (†).
 (ii)
When aligning a family G with structure (†) to some other family F, we should aim at finding alignment that is good mainly over G’s conserved regions, because G’s sequences are quite different elsewhere and even biologists may not know how to align the sequences correctly over there. Furthermore, since G’s sequences are very similar over the conserved regions, having a good alignment (over the conserved regions) for one sequence of G will essentially give us good alignments for all the others. This suggests that when aligning G to F, we may proceed as if we were aligning a single (meta)sequence to F (or more concretely, assume that G has only one single sequence).
Observation (i) motivates the following strategy to determine whether a family has structure (†): If the standard deviation of the PIDs of the family is sufficiently small, we bet that it has structure (†). For ease of reference, we will say that such family has low PID discrepancy, or simply low discrepancy.
Note that (2) is equal to (1) when C _{ i }=C _{ j }=1, or when both C _{ i } and C _{ j } can be regarded as containing only one single sequence (metasequence), as suggested by Observation (ii) for families with low discrepancy.
For distantly related sequences, they are only similar at some local domains or motifs, and these homologous regions may be rather small and are hidden in some long divergent regions. This causes troubles for the progressive alignment method, which is based on global pairwise alignments to merge and align iteratively clusters of sequences together to construct the MSA, and the order of merging depends solely on the guide tree. By insisting global alignments for inputs that have only local similarity, the progressive method may introduce, even in the early stage of execution, many misaligned columns and other mistakes, and these early mistakes cannot be corrected and may be propagated [20] and create more mistakes. To improve the alignment quality for distantly related sequences, we forget about the progressive methods and instead, we try nonprogressive ones.
There exist many nonprogressive MSA methods. For example, the nonprogressive sequence annealing technique described in [21, 22] combines successively confident alignable regions to build up the multiple alignment; the most similar segments (even in small size) will be aligned first in order to preserve those conserved motifs or domains.
We use this sequence annealing technique to handle input of distantly related sequences. Recall that in Stage 1, we have used the adaptive method to determine substitution scores. During the process, we have also found, for every pair of sequences x and y in the family, and every 1≤i≤x and 1≤j≤y, the probability Pr(x _{ i },y _{ j }) of aligning the ith character of x and the jth character of y in the best alignment. To construct an MSA for distantly related sequences, we will first sort all the character pairs (x _{ i },y _{ j }) in descending order of Pr(x _{ i },y _{ j }). Then, starting from the first character pair in the sort list, which has the highest probability of being aligned at the same column, we follow the character pairs in the list and try to insert each pair to the alignment (or more precisely, make the two characters in the pair aligned at the same column) one by one. However, we will actually make the insertion only if the alignment is still consistent after the insertion.
 (i)
introducing a new samecolumn set (when both x _{ i } and y _{ j } are not currently in any samecolumn set), or
 (ii)
adding either x _{ i } or y _{ j } in some existing samecolumn set (e.g., if y _{ j } is already in some S, then we need to add x _{ i } to S after inserting (x _{ i },y _{ j })), or
 (iii)
merge two samecolumn sets (e.g., if x _{ i } is already in S and y _{ j } in S ^{′}, then after inserting (x _{ i },y _{ j }) we need to merge S and S ^{′} together).
We also need to update the edge set of the graph to reflect the changes. Note that we will not actually make the insertion unless the updated graph is still acyclic, which means that the column constraints are still consistency. When we have finished processing all the character pairs in the sorted list, we topologicalsort the graph to get a skeleton of the MSA. We obtain the final MSA by adding to it those characters not in the skeleton. See [16, 21–23] for more details.
Methods
Construct better guide trees for normally related sequences

We first classify the input families according to their σ(PID)s, and for each group i, i.e., the group with σ(PID) =i, we compute the average TC scores \(\overline {TC}_{\tt WPGMA}\) and \(\overline {TC}_{\tt UPGMA}\) over the alignments returned by GLProbsWPGMA and GLProbsUPGMA for the families in this group, respectively. Then, we compute \(\Delta _{i} = \overline {TC}_{\tt WPGMA}  \overline {TC}_{\tt UPGMA}\).

We put a point (h,k) on the curve if \(k =\sum _{i \leq h}\Delta _{i}\), i.e., the accumulated differences up to the group with σ(PID) =h is k.
Note that if the curve is increasing at (h,k), we have Δ _{ h }>0 and GLProbsWPGMA is doing better than GLProbUPGMA. As shown in Fig. 2, the accumulated differences is mainly increasing until σ(PID) reaches around 11.5 %, and hence GLProbsWPGMA is doing better up to this point. Afterwards, the curve is decreasing, which means GLProbsUPGMA is doing better. Therefore, as default, PnpProbs decides that a family has low discrepancy if its σ(PID) is smaller than 11.5 %, and uses the WPGMA method to construct its guide tree.
Nonprogressive alignment for distantly related sequences
The algorithm of PnpProbs
 1.
Calculate the percent identity (PID) for every pair of sequences, and compute the average avg(PID) and standard deviation σ(PID).
 2.
Use the avg(PID) to determine proper pairHidden Markov model(s) to compute the posterior probabilities.
 3.
Transform the posterior probabilities for consistency and use them as substitution scores.
 4.
Based on avg(PID) to determine which alignment approach to use:
If avg(PID) <18 % (this is the distantly related sequences case, and we use the nonprogressive sequence annealing technique to get the MSA) (a)
Sort the probabilities P(x _{ i },y _{ j }) in descending order.
 (b)
Construct an acyclic graph with the samecolumn sets as its nodes, and insert the character pairs (x _{ i },y _{ j }) to the graph iteratively according to the sort probabilities.
 (c)
Topologically sort the graph, and from it constructs the MSA.
If avg(PID) ≥ 18 % (this is the normally related sequences case.) (a)
Compute the distance matrix for every pair sequences.
 (b)
Determine the guide tree construction method based on some threshold τ on the standard deviation σ(PID) of the PIDs, whose default value is 11.5 % as suggested by our study in Section “Construct better guide trees for normally related sequences”: If σ(PID) <τ, use the WPGMA method to construct the guide tree; otherwise, use the UPGMA method
 (c)
Based on the constructed guide tree, perform the profiletoprofile alignments to construct the MSA.
 (a)
 5.
Refine the MSA given in the previous step as follows: we iteratively divide the MSA into two groups by randomly assign each sequence one of them, and we realign these two groups using standard profileprofile alignment method to see if any improvement can be made. We stop when either (i) we have made 2N iterations and still cannot make any improvement, or (ii) we have made 4N iterations. Here, N is the number of input sequences.
Results
To evaluate the performance of PnpProbs, we have compared it with thirteen other leading multiple sequence alignment tools on three popular benchmark databases. PnpProbs has the best performance in almost all cases, and it achieves significant improvements over the other tools on distantly related sequences. We have also studied its practicability by using it for phylogenetic analysis.
Benchmark comparison
We have compared PnpProbs with the following multiple sequence alignment tools, ten of them use the progressive method: ClustalW 2.1, TCoffee 9.03, MAFFT 7.031, MUSCLE 3.8.31, ProbCons 1.12, CONTRAlign 2.01, Probalign 1.4, MSAProbs 0.9.7, Clustal Ω 1.1.0, GLProbs, and three of them use the nonprogressive method: Alignm 2.3, PicXAA, DIALIGN. We used these tools to align families of sequences obtained from the three benchmark alignment databases, namely OXBench 1.3, SABmark 1.65 and BAliBASE 3.0. To measure the accuracy of their alignments, we used the sumofpairs score (SP) and the totalcolumn score (TC), which were commonly used in previous studies [2, 10, 11, 13, 15].
Average SP and TC scores on OXBench
ALL (0–100 %)  0 %–20 %  20 %–50 %  50 %–100 %  Time  

SP  TC  SP  TC  SP  TC  SP  TC  mm:ss  
PNPProbs  90.41  82.23  48.98  24.88  83.47 ^{∗}  68.79  98.05  95.18  2:58 
GLProbs  90.38 ^{∗}  82.14 ^{∗}  47.29 ^{∗}  22.95 ^{∗}  83.48  68.65 ^{∗}  98.05  95.18  3:15 
MSAProbs  90.07  81.75  44.83  22.08  82.77  67.74  98.01  95.08  4:04 
Probalign  89.97  81.68  43.58  20.51  82.53  67.46  98.05  95.18  2:10 
CONTRAlign  89.34  79.87  44.76  17.83  81.56  64.75  97.55  94.10  10:19 
ProbCons  89.68  80.86  44.15  20.30  82.06  66.33  97.84  94.61  1:48 
MUSCLE  89.50  80.67  45.64  21.90  81.75  66.15  97.63  94.28  0:19 
MAFFT  88.00  77.96  37.82  13.27  78.99  60.86  97.41  93.68  0:19 
TCoffee  89.52  80.50  43.99  19.11  81.82  65.85  97.75  94.38  15:05 
Clustal Ω  88.91  79.99  39.09  16.38  80.71  64.49  97.76  94.58  0:12 
ClustalW  89.43  80.16  42.94  18.23  81.67  65.01  97.76  94.40  0:22 
PicXAA  89.64  80.74  45.11  22.04  81.86  65.91  97.84  94.55  4:26 
DIALIGN  83.97  72.41  26.03  8.07  72.67  52.57  95.21  89.54  3:17 
Alignm  86.95  76.06  28.36  12.74  76.35  57.54  96.95  92.60  21:14 
Average SP and TC scores on SABmark
ALL  Twilight Zone  Superfamily  Time  

SP  TC  SP  TC  SP  TC  mm:ss  
PnpProbs  61.37 ^{∗}  41.70  44.40  24.80  67.19 ^{∗}  47.49  3:00 
GLProbs  61.42  41.36 ^{∗}  44.35 ^{∗}  24.30 ^{∗}  67.27  47.21 ^{∗}  3:20 
MSAProbs  60.27  40.02  42.97  22.88  66.20  45.90  1:58 
Probalign  59.53  38.63  42.42  22.64  65.39  44.11  1:01 
CONTRAlign  57.45  35.59  39.01  17.69  63.77  41.73  4:56 
ProbCons  59.69  39.17  42.81  22.78  65.47  44.79  1:12 
MUSCLE  54.51  33.47  34.69  16.96  61.29  39.13  0:46 
MAFFT  52.63  32.57  31.72  15.17  59.79  38.53  0:22 
TCoffee  59.14  39.53  41.66  23.29  65.13  45.10  4:36 
Clustal Ω  55.02  35.47  35.55  18.10  61.69  41.42  0:18 
ClustalW  51.92  31.37  31.45  15.09  58.93  36.95  0:14 
PicXAA  59.37  39.11  41.05  21.51  65.65  45.14  3:29 
DIALIGN  47.09  27.11  27.85  12.73  53.69  32.05  1:03 
Alignm  46.19  31.07  25.72  16.28  53.21  36.14  5:32 
Average SP and TC scores on BAliBASE
ALL  RV11  RV12  Time  

SP  TC  SP  TC  SP  TC  mm:ss  
PnpProbs  82.80 ^{∗}  68.00  68.91  45.73  94.79 ^{∗}  87.23 ^{∗}  3:22 
GLProbs  83.20  67.59 ^{∗}  69.72  44.68  94.84  87.38  4:05 
MSAProbs  82.35  66.83  68.13  44.02  94.63  86.52  3:02 
Probalign  82.53  67.27  69.50 ^{∗}  45.34 ^{∗}  94.63  86.20  1:47 
CONTRAlign  77.59  58.10  61.78  35.60  91.23  77.52  6:37 
ProbCons  81.55  65.22  66.99  41.68  94.12  85.54  1:41 
MUSCLE  75.60  58.27  57.15  32.06  91.53  80.89  0:37 
MAFFT  72.46  52.58  52.96  26.19  89.30  75.38  0:14 
TCoffee  80.82  64.93  65.63  41.36  93.94  85.29  5:18 
Clustal Ω  75.96  59.38  59.01  36.21  90.60  79.38  0:21 
ClustalW  69.63  49.21  50.06  22.99  86.52  71.84  0:21 
PicXAA  81.33  66.08  66.56  44.06  93.47  84.19  3:26 
DIALIGN  68.63  48.22  49.72  26.81  84.18  65.81  1:34 
Alignm  71.45  56.04  51.88  33.06  88.36  75.88  7:09 
Phylogenetic analysis
To compare the practicability of PnpProbs with other existing tools, we have used it, as well as five other MSA tools, namely GLProbs, MSAProbs, PicXAA, MUSCLE and ClustalW, to construct phylogenetic trees. Given a set of sequences, we first used the six MSA tools to construct six MSAs, and used them as input to the Maximum Parsimony method [24] to infer six hypothesized phylogenetic trees. Then, for each of these hypothesized trees, we calculated the RobinsonFoulds(RF) distance [25] between the tree and the model phylogenetic tree; the smaller the distance, the closer the two trees, and hence the better the corresponding MSA. Our tests used input sequences chosen from two benchmark databases, namely YuleHarding tree simulated data [17] and SABmark empirical data [5].
Simulated data
Empirical data
Discussion and Conclusions
Our MSA tool PnpProbs aims at combining the strength of progressive and nonprogressive methods for multiple sequence alignment; it uses progressive method for normally related sequences, and uses nonprogressive method for distantly related ones. In [1], we proposed to use the average percent identity to estimate the similarity of a family of sequences, and in this paper, we proposed to use the standard deviation of the percentage identity to estimate the discrepancy of a sequence family. For normally related sequences, PnpProbs uses different methods to construct guide trees depending on the discrepancy of the family. Our experimental results showed that PnpProbs has the best TC scores in all but one test. We have also evaluated PnpProbs’ practicability, and our results suggested that PnpProbs will be a useful tool for downstream phylogenetic analysis.
For possible future research direction, we note that most of the MSA tools try a certain range of sizes of components to assemble multiple sequence alignment. For example, the progressive alignment method uses big components of sequence profiles, and the nonprogressive sequence annealing technique uses small components, e.g., alignable columns or residue pairs. A natural research direction is to consider multiple sizes of decomposed components in one algorithm to build up the MSA such that families of sequences with long conserved regions apply large components and those with small conserved patterns use small components.
Declarations
Acknowledgements
Lam was partially supported by GRF Grant HKU716412E. Ting was partially supported by GRF Grant HKU713512E.
Declarations
This article has been published as part of BMC Bioinformatics Volume 17 Supplement 8, 2016. Selected articles from the 11th International Symposium on Bioinformatics Research and Applications (ISBRA ’15): bioinformatics. The full contents of the supplement are available online https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume17supplement8.
Funding
Publication costs for this article were funded by the authors’ departmental resources.
Availability of data and materials
PnpProbs can be downloaded from https://github.com/ytye/PnpProbs, and the data used in our experiments can be accessed in [17, 18].
Author’s contributions
HFT conceived the project, YY, TWL and HFT designed the project, and YY implemented the project.
Competing interests
The authors declare that they have no competing interests.
Consent for publication
Not applicable.
Ethics approval and consent to participate
Not applicable.
Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Authors’ Affiliations
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